Have you been playing away games?

If so you will lose money with no home games, assuming your prize money doesn't cover your wages. Currently I pay out a tad over 9M in wages a day - and when only playing away in the league only get a little over 1.5m in prize money - thus losing 7.5m a day when only playing the one away game for example.

If you sacked a player to make room for your new player then you will have lost money there too - also if you have renewed player contracts etc...