Paris, 1121 :
...Around the year 1120, [Peter] Abelard published a little essay on the Trinity that was to prove more damaging to him than all the knives of Heloise's avengers [....]
Abelard "has defiled the church," [Bernard of Clairvaux] wrote to a Roman cardinal, "he has infected with his own blight the minds of simple people."
[Charged in absentia], Abelard arrived the next morning for the disputation only to find that the format was that of a trial.... He declined to participate in the proceedings and appealed directly to the pope to decide the issues presented....Innocent II condemned him as a heretic, excommunicated his followers, ordered his books to be burned in Saint Peter's Square, and commanded him to retire to a monastery, there to be perpetually silent. 
Paris. Unknown date, 1192-1203 :
From the Chartularium universitatis Parisiansis.
Letter from Stephen, Bishop of Tournai 1192-1203, to the Pope:
The studies of sacred letters among us are fallen into the workshop of confusion, while both disciples applaud novelties alone and masters watch out for glory rather than learning. They everywhere compose new and recent summulae and commentaries, by which they attract, detain, and deceive their hearers, as if the works of the holy fathers were not still sufficient, who, we read, expounded holy scripture in the same spirit in which we believe the apostles and prophets composed it. 
Oxford, c.1380 :
When [John Wycliffe's] doctrine on the Eucharist appeared, the friars and monks, the orthodox theologians of the place, united with the Chancellor Berton and a few seculars to condemn the thesis. A university officer was sent into Wycliffe's lecture-room to enjoin silence upon him. There he was found, propounding to his audience the impossibility of accidents without substance, and of the other metaphysical absurdities which he alleged against Transubstantiation. He appeared to be a little taken aback at the decree, but replied that it could not shake his opinion. 
University of Pavia, 1433 :
On Sunday, January 22, 1433 a public examination of a candidate in law was in progress in the cathedral. At the point in the proceedings where anyone in the audience might oppose granting the degree [Professor of Rhetoric, Lorenzo] Valla rose and apparently did exactly that, no doubt with sharp comments about the ignorance and barbarous language of the legist....The presiding bishop ordered Valla's arrest for precipitating the breach of decorum. Valla fled the church with law students in hot pursuit.
In one night in February 1433 Valla wrote a slashing attack denouncing the practice and teaching of civil law and its major figures, the revered Accursio, Bartolo, and Baldo degli Ubaldi. ... His was the first of several humanist attacks on traditional legal studies. 
University of Padua, 1555 :
While at Padua, [Professor of civil law Matteo Gribaldi Mofa] made little secret of his religious views. He did not attend mass, probably expressed himself freely, and opened his home to ultramontane Protestant students.. He also spent his vacations at his castle in Protestant Switzerland. The Paduan bishop became suspicious and Gribaldi's concurrent [i.e, fellow professor] denounced him. [Refusing to rebut the allegations] Gribaldi left Padua on April 25 1555. The University of Tubingen in Lutheran Wurttemberg immediately hired him....Gribaldi further developed his anti-Trinitarian views and arguments for religious toleration....and he lost that position in 1557....The Catholic University of Grenoble hired him for the second time in 1559. As at Padua, fellow professors denounced him for his religious views, but academic differences may also have separated them....Gribaldi again lost his professorship and retired to his Swiss mountain home, where he died in 1564. 
University of Bologna, 1570 :
On October 6, 1570, the Bolognese Inquisition arrested Girolomo Cardano, first ordinary professor of medical theory at Bologna....Without the trial records of the Bolognese Inquisition (of which little survived), it is not possible to determine which ideas were found objectionable and which errors he abjured. Certainly Cardano expressed views that ecclesiastical authorities might have found offensive. He strongly endorsed astrology and prepared a horoscope for Christ. He held Christianity to be the true religion but criticized religious writers, especially in the early church, for foolish statements. He wrote a defense of Nero in which he noted that the criteria for judging historical figures were historically conditioned and often wrong. He marveled at men who willingly endured martyrdom for various religious systems, not just Christianity. At times, Cardano seemed to adopt a relativistic view toward the world's religions, and he seemed indifferent to the institutional church. 
Harvard, 1700 :
At last, in 1685, Increase Mather came to the rescue by consenting to assume the place [of Harvard President] temporarily, giving it such time as he could spare from his duties as minister of the Second Church of Boston. [...] This was wholesome neglect, for it left the running of the college in the hands of the two tutors, John Leverett and William Brattle, both of them able, liberal and broadminded men. Excellent teachers, sharing their enthusiasms for science with their students, they labored to make Harvard a liberal arts college abreast of the best English standards. [...] Had Mather been more observant of what was going on under his very nose and less concerned with buttressing the control of the orthodox group over the college by means of a new charter, he might have checked this liberal drift. 
By the later years of the decade Mather had come to worry about the direction of the college -- the liberal direction. ... [In 1700, Mather] issued his Order of the Gospel, an effort to recall to New Englanders the great charge that history had given them.
Let the Churches pray for the Colledge particularly, that God may ever Bless that Society with faithful Tutors that will be true to Christ's Interest and theirs, and not Hanker after new and loose ways. This is a matter of no small concernment. For if the Fountain whose Streams should make glad the City of God, be corrupted, Posterity will be Endangered thereby. 
Hungary, First Obstetrical Clinic of Vienna General Hospital (teaching clinic for university medical students), 1847 :
A young Hungarian physician named [Ignaz] Semmelweis...observed how frequently puerperal fever occurred in patients attended by students who were accustomed to go directly from the autopsy room to the maternity ward, and he came to the conclusion that uterine infection is caused by matter introduced into the birth canal from outside sources, through the hands of the nurse, doctor or other attendant. He succeeded in greatly reducing the amount of puerperal fever in his maternity clinics by the simple measure of requiring all attendants to wash and disinfect their hands before examining a patient. Other doctors were strongly opposed however to the ideas of Semmelweis and his methods were never widely adopted or well-known until long after the independent work of Lister (beginning 1864) had finally brought about the general use of antiseptic techniques. 
At the time, diseases were attributed to many different and unrelated causes. Each case was considered unique, just as a human person is unique. Semmelweis's hypothesis, that there was only one cause, that all that mattered was cleanliness, was extreme at the time, and was largely ignored, rejected or ridiculed. He was dismissed from the hospital for political reasons and harassed by the medical community in Vienna, being eventually forced to move to Pest 
 Richard E. Rubenstein, Aristotle's Children (Harcourt, 2003), pp. 116-125.
 Lynn Thorndyke, translator and editor, University Records and Life in the Middle Ages (Norton, 1944, 1975), pp. 22-3.
 George Macaulay Trevelyan. England in the Age of Wycliffe (Longmans Green and Co., 1948), p. 298.
 Paul F. Grendler, The Universities of the Italian Renaissance (Johns Hopkins, 2002), pp 210-11.
 Grendler, pp. 187-8
 Grendler, pp. 188-9
 Thomas Jefferson Wertenbaker, The Puritan Oligarchy (Scribner, 1947), pp 152-3.
 J. David Hoeveler, Creating the American Mind: Intellect and Politics in the Colonial Colleges (Rownman & Littlefield, 2002), p. 47-9
 Increase Mather, Order of the Gospel Professed and Practiced by the Churches of Christ in New-England (1700, undated Kessinger reprint), p. vi
 Kenneth R. Burdon and Robert P. Williams, Microbiology (Macmillan, 1968),
 Wikipedia, s.v. "Semmelweis."