I think because i still am depressed and have suicidal thoughts sometimes he said it would take away the negative thoughts.
Wellbutrin is a very stimulating antidepressant which can lift moods, it can also trigger panic attacks in those with anxiety disorders. Moreover, like all the other antidepressants it won't work immediately. A mood stabilizer might be better.
Is it unusual to experience neg thoughts? Do they usually pass?
Yes, and yes. You're being put through the emotional wringer, partly by your mind and partly by the med, so it would be unusual if it didn't all get you really down from time to time. Unfortunately, there are no instant cures. It will take time to put your life back together. Until then just take it a day at a time, or even second by second if necessary. Endure, until things begin taking a turn for the better. They nearly always do, IME.