If all the other branches are fine and not showing signs of trouble, and you haven't figured out what's wrong with the first two, then I might consider cutting them because whatever it is, you don't want it to spread (if it is spreadable!). The symmetry as things stand now might be cockeyed, but then what can you 'see' in the tree without them that you could turn around to be maybe more interesting than it's been until now? Maybe a whole new direction, or style!

Lucy 5
Thanks for the advice, we have no bonsai experts locally so I am pretty much on my own here lol.

My Fukien Tea has three branches that I'm not sure about, the main branch comes up straight from the soil, then takes a 90 degree turn, then straight up, with a few small branches at the top.
But there are three branches coming off of the main branch. First one right where it bends, and two others where the main branch goes straight up.
It's in pretty good health with small leaves and flowers, but those two branches are bugging me, and I feel they should be gone.
I bought this one at a big box store for $10.99, and looking on line one like this goes for over $500.00, did I get a good price?
Wish I could post a photo of it here, but I don't see a link to upload it. Anyone?