Hello Katarina,
I think, that the problem can be in the Flow Regime or in the Manning´s values.
1. You could check a Freude number, if these values are around 1, so you have to use a mixed flow regime.
2. The error can be also in the Maninng´s values- roughness parameters. If you defined high values or you have big difference between channel n-value and floodplains n-values in the CS.
Let me know, if my proposal help you.
regards
Robert