UPDATE: It has been fixed.
We went today to prefectura, me, my bf, and our friend's brother and uncle. The young nice guys who kept my roll the other day were not there, instead there were two older and much more serious guys (!!!!) but luckily at least one of the guys from Monday was there today so he could corroborate that I really went and really left the roll because surprise surprise - THEY LOST THE ROLL. We waited and hour while they looked through all their papers, then we went outside to wait because they had stopped looking and we thought we might be there all day, but then the guy comes out of another building with the roll in his hand. Finally they checked us all back into the system and gave me my stamp. They gave the captain (my friends uncle) a bunch of flak for waiting 7 days and that the rule is 'within 24 hours' but I honestly think it would have been worse if they hadn't lost the roll and not been able to find it for an hour. The guy seemed really annoyed/embarrassed so it was a little bit to our advantage (besides making my heart rate go up for an hour while we waited).
In the end I have two existing doubts:
The dates on my stamps are all messed up. My salida from Arg is dated Apr 18. My entrada and salida from Uruguay are dated Apr 20. My entrada back to Argentina is dated Apr 26. If anyone in the future asks at customs why that is, I'll tell them that about going to Uruguay in a boat and say that when we came back, I didn't get my stamp because the guy forgot (true for the salida at least, he had forgotten even though we did stop in prefectura on the way out to UY) and that I had to sort it out a few days later. Another plan is to stop using my European passport and just pay the damn fee to use my US passport next time I enter from the states, and thus avoid raised eyebrows.
Second thing is, the stamp he gave me today doesn't say 90 days, doesn't say anything. He didn't even mark the box to indicate which visa it was. Do I leave it blank? Should I circle the box next to "TA" myself or just leave it as is? Again, trying to avoid raised eyebrows or any future awkward conversations at the customs window.