My name is Muhamed A. Sewidan, I'm a physicist. My first name is spelt in my passport and transcripts (Mohamed) with o, and in my published papers (Muhamed) with u.
Can this cause me any trouble?
You can probably ignore the spelling in your passport as it isn't linked to your IP. Use a consistent spelling in your academic work and you should be fine. The people who need to find you as an academic will be able to find you.
I can't imagine when your choice of spelling in papers would ever come up if it doesn't match your passport. Moreover the transcription between different language systems isn't particularly consistent. People recognize this.
Transcripts is similar if not identical, but the times you need to verify that you are indeed the author of a set of papers (changing jobs, for example) is still pretty rare. And a simple explanation should suffice.
There are people who publish under a pseudonym unrelated to any legal name. And legal names can change for many people.
Irrelevant anecdote: My Taiji tradition has two living (senior) masters. They are brothers, both born in China. One of them has family name Tung, the other Dong. They are pronounced the same, but not like the English forms suggest - something intermediate. They immigrated to the US at different times, met different immigration authorities who wrote down different family names based on the sound. There isn't an obvious way to translate written Chinese characters into English in such a case. We cope.