not sure how you run into this first problem... either needed a space before the trade or immediately after to avoid the situation altogether. dump a bench player or 7th reliever that can be easily replaced at virtually any time (more so with the bench batter), etc... when you forget. or... just stop forgetting,
you already know the answer it seems: create a better habit.
50round amatuer draft might require roster limits... never had so many new players rcreated every year... i'd also be concerned about flat stats, based on how this game engine works, if it floods your league with a ton of high-end talent. e.g. players with 70+power could turn into low-20's home run players etc. and be very consistent about it because too many are amazing HR hitters (HR are anything but consistent results).
like mitch said, leave the lowest tier unlimited then i'd suggest 25-30 for AAA, 30-35 for A/AA... maybe 40 for Short A and lower if you have them and not the lowest tier of course. the higher the league, the clsoer to your MLB roster limit - whatever it is. helps cut the fat of lower-rated players as you get near the bigs.
definitely make sure the setting in Stats and AI section for EACH minor leauge is set to play potential as opposed to current ability - similar words not exactly as i wrote them. drop down box on left side of screen, only visible for minor leagues, not Major leauges.
that way, even if you have 50 players on a team, the best potential players will get playing time.