Hi
If you are a PR for 2 years, why don't you have a PR card?
Did they tell you when they seized your travel document that there would be some kind of hearing on your case? You should not apply for citizenship if your PR status is in question.
1. He probably has a PR card, but doesn't have his countries passport. So he was issued a Canadian Travel Document, which bars you from visiting the country that you claimed refugee status against. CBSA could take the attitude that he has now committed "refoulement" and they may apply to vacate his refugee claim.