If this was a game breaking bug we'd have about a thousand threads about it, we don't though. Late goals are common in real football and so are common on the game, its a bummer but its up to you to deal with it. Might I suggest buy some defender's with high a concentration stat. Low concentration and they will start to switch off towards the end of the match.
I agree it happens. My very own Spurs suffered this season in real life. After we lost 2-1 to Everton after being 1-0 till 85th minute I read a stat where if games ended after 80 minutes we'd be top of the league. But we've cut that out and also this has happened over one and a bit seasons, 90% of the time. I don't mind losing or drawing, as I said before, I don't expect to pick a tactic that wins everything, but when it's constantly at the same point in games and nothing I do can stop it...meh. I've now won 2 on the bounce, 1-0 wins, playing a lot deeper and more rigid, so we'll see how it goes. I may make the play off's as I'm 2 points behind but i'm 18 off top spot...if only those goals hadn't gone in.