Found this on the NCAA website, take note of the Play situation at the bottom.
Rule 3-4.6, BR-51.
Clarification that the only time substitutions are not allowed in the last 59.9 seconds is on a timer's mistake or an inadvertent whistle. If the whistle is blown for other reasons substitutions are allowed. Examples:
Clarification of a two- or three-point goal
Net getting caught up on basket
Correctable error
Book error (scorer forgets to inform official of player's fifth foul)
Injury, blood, disqualification
If a timeout is requested when play is stopped for a timer's mistake or an inadvertent whistle, substitutions will be allowed.
Play: Ball rolls past the bleachers on an open ended court during the last 59.9 seconds of the second half and the official blows the whistle.
Ruling: Official should deem this an inadvertent whistle and substitutions should not be allowed to enter the game. The clock is stopped. There is no need to blow the whistle
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