Minnesota is reporting problems processing tax returns submitted through the online TurboTax program, and while Wisconsin tax officials say the problem has not been reported here, some residents may be affected.
The State Department of Revenue says 50,000 people live in Wisconsin but work in Minnesota.
Spokeswoman Laurel Patrick says Wisconsin does not track how many of them use the program TurboTax to file. Minnesota has reported problems with 11,000 state income tax returns.
Minnesota and Wisconsin used to have a reciprocity agreement that let people who live in one state but work in another file where they reside. That ended in 2009.
"Wisconsin residents who work in Minnesota have to file a Minnesota state income tax form. And so we've been working to restore income tax reciprocity and we very much want to. But there's one issue with Minnesota that they haven't been able to drop yet, for us to fix that issue."
Minnesota wants an extra $6 million from Wisconsin per year.
Patrick says the "glitch" with TurboTax is isolated to Minnesota and that e-filing is still the fastest way for taxpayers to get refunds.