Can a flotilla use a engineering command dial and a engineering token to repair 2 points of damage on a friendly ship?

I don't think so because I thought if you resolve the engineering command you have to combine the token and dial. Also because a command can't be resolved twice and an effect can't happen twice during an event.

Am I wrong or right?

You cannot resolve it twice. Resolving the dial and token counts as a single command, and you cannot resolve the same command more than once.

So you are better off resolving a token to repair.