Parent company Birmingham International Holdings Limited blamed "fractious and inharmonious relations within the management" for Tuesday's decision to go into receivership.
The Championship side could lose 10 points if the Football League decides it was an "insolvency event".
"That's something we're hoping won't happen," he told BBC WM 95.6.
"I just hope people see it might be a way of moving forward - it doesn't mean the club suddenly haven't got the money to continue."
A 10-point deduction would lower Birmingham into the Championship relegation zone.
Despite that, Rowett says his players must ignore any off-the-field matters if they are to build on their form since he joined the club in October.
Wednesday's 1-1 draw with Championship leaders Middlesbrough lifted his side to 12th in the table; the Blues were in the bottom three when he took over.
"I think we've made huge strides," he said.
"We were three or four points adrift of safety and now we're sat mid-table and nine points clear.
"We want to achieve more now and that's got to be from full focus on the pitch and not worrying about anything off the pitch that might spread a little bit of negativity."