What complication has occurred that makes Charlie so aware of time passing?

Charlie becomes aware of the passing time because he learns that Algernon is beginning to forget..... foreshadowing his own loss of memory or knowledge.

I went into the lab where Burt was watching Algernon in one of the multiple problem boxes. He sighed and shook his head. "He's forgotten a lot. Most of his complex responses seem to have been wiped out. He's solving problems on a much more primitive level than I would have expected."

"Of course, taking you on in this experiment was a serious responsibility. I don't know how much you remember or how much you've pieced together about things in the beginning of the project, but we tried to make it clear to you that there was a strong chance it might be only temporary"