This happen to me, and with commissioner mode, I went in and edited(increased) the salary of several of my players until I was over the floor. Stinks, but is the only way I could move the game forward.
What I did in my next game, was to sim one year, then on July 1st, I went in and reduced the salary cap floor drastically. I then expanded the league and took over an expansion team. I like taking over expansion teams, but won't be doing it in year one anymore.
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