I've seen this happen a lot, with my teams and a few times with my Dad's teams. And it resulted in a loss every time. A couple seasons ago it happened against #1 Illinois. I was up by one, my guy fouled with one second left, and I lost by one. It was heartbreaking.

Does anyone know why this seems to happen so often?

I haven't really noticed a trend on my teams with fouling more often at the end of the game, although something similar did happen to me a few days ago.

In real life basketball, the ref would be less inclined to call a foul at the end of the game, especially if you're team was on defense playing at home.

One reason may be that your team is fatigued towards the end of the game, which would result in more fouls.

I saw a team in a tie game foul on the floor with no time on the clock and lose...

There sim engine sometimes doesn't account for logic.

in real life, some observers say the refs should call the game the same in the first minute and last minute.

Only in a SIM does that actually happen

I lost in the NT last year with my DII team when my A IQ senior player with a decent def. rating fouled somebody with no time left on the clock. It sucked.