Reproduced on the first German long campaign scenario. Normally you get the "Victory" popup after either killing the last enemy unit or taking the last objective. However, if you are clicking quickly, it's possible to kill the last unit and then immediately take the last objective before hitting OK on the Victory popup.
This causes you to skip the next scenario. Doing it at the end of Madrid immediately takes you to Suomussalmi, bypassing Poland entirely. I assume you're incrementing the scenario counter on each end-of-scenario action without checking to see if it's already been done.