As most of you remember, there was a P. S. on the letter. It's possible that he (Lecter) sealed the envelope, but opened it back up to add the P. S., and sealed it with the wax seal.
If you watch one of the deleted scenes from the DVD version of Hannibal, it shows Hannibal actually put the wax seal on the envelope. After cutting that scene it does appear to be a flaw. But its not!
I noticed that particular slip up as well.
No, it was the same envelope, first it showed Clarice opening the envelope, with a knife, only breaking the seal, while the rest of the letter was obviously not stuck down. Then it showed Hannibal writing the letter, and then licking the exact same envelope that Clarice opened with the knife. Even if he did put a seal on it afterwards, i doubt he would have opened it as it would have torn. Although envelope adhesive isn't very strong, at least one section of the envelope would have been left sealed where he licked it. This was definitely a major slip up.
I agree with Vee. If everyone would watch the deleted scenes before replying, they would see that in one of the deleted scenes, it shows Hannibal Licking it, and then adding the seal. When this was removed from the movie, you no longer saw him use the wax seal, but he still did BOTH.