The best thing to do about intrusive thoughts is to just let them pass through one ear and out the other, concentrating on your prayers. You can whisper a little, "Help/forgive me, Lord Jesus" if you want to. Don't let that phrase become a meaningless mantra, however. But simply move on.
The worst thing to do about intrusive thoughts is to focus on sweeping them out of your mind. The more your think about them - how bad they are, where are they coming from, and getting rid of them .... the more they hang around and come back later when you are doing the same thing.
I have intrusive thoughts and so do a terribly large amount of people. It's not always during prayer time, but could be anytime.
For the Christian, they can be from annoying to frightening. Just remember, God KNOWS your heart and if you are saved, God KNOWS that these thoughts do not reflect your salvation and assurance in him.