If you have the first situation, then that is not possible. The app might have a problem. Or, the images you are using to create the supercube might be the problem. Some pieces that look similar could be confused and put in the wrong places.
If you have the second situation, this is what you can do.
Move the four pieces into the same face. Something like this.
Then do (m U2 m' U2)x3 U (m U2 m' U2)x3 U'
Lastly, put the pieces that were moved back to where they were.
CogitoErgoCogitoSum wrote:So if there is a way to rotate all four center edges 90 degrees around without rotating the center corners then Im set.
I don't think that there is. If these four pieces are the only unsolved pieces on the puzzle, I think there's a problem. Some other pieces on the puzzle are probably not correct. As I mentioned before, some pieces may be confused for others. Also, check the centerpieces. It may be that some are rotated incorrectly.