Answer:
Sister Aloysius believed that some sexual misconduct had happened between Father Flynn and Donald Mueller.
The history of infringement upon Father Flynn from his previous job makes Sister Aloysius assume that such inappropriate conduct have taken place.
Step-by-step explanation:
"Doubt" is a play written by John Patrick Shanley. The play is based upon the theme of doubt, as delievered in the sermon by Father Flynn.
When Sister Aloysius comes to know that Father Flynn has been protecting Donald Mueller, she suspects of some sexual misconduct between them. She assumed that Father Flynn might be abusing Donald Mueller sexually.
Sister Aloysius is doubtful of such conduct taking place because she has heard a rumor about Father Flynn from his previous job that he was caught in some act of infringements. This leads her to believe that some misconduct has happened.