Sure - the example that I noticed most recently (because I was at PDXCon!) is Hearts of Iron 4. For an older example, Panzer General 2. Many games use the iron cross on a red background and leave you with the idea that you saw a swastika, when you didn’t.
I’m certainly not saying “no game has ever used a swastika” (I assume without checking that Wolfenstein 3D did, and I know the original Apple II Wolfenstein did.) But enough noticeably don’t use it that it’s part of this discussion.
EDIT: Had to look this one up. The recent game Return to Castle Wolfenstein, which is a game about killing Nazis, does not have swastikas in it.