Pursuing the logic of the above, using "vent blockage" as a core problem, it will manifest itself as a sometimes-open drain letting sewer air into the house. One of the drain holes is letting sewer air into that bathroom at night. A drain has a P trap to prevent this. Thus, one of the P traps is being "siphoned" or emptied. Tape shut one of the drains. Use masking tape. See if that one is the one letting sewer gas in at night. Try again with another drain. Repeat. If the only drain hole is the bathroom sink, you only have one drain to stopper, to try this. The seal must be perfect. Use tape. In the morning when you take the tape off, the P trap will still have its water in it so you will not smell gas there even if you try real hard. Once you have done this testing, it will confirm to you what the problem really IS. This is valuable knowledge. It enables you and your plumber to know clearly what to do next. Report your findings and await further instructions.

If the wax ring is not sealed to the closet flange, could sewer gas be entering from that end? Picture this scenario: A tiled floor with a finish height higher than the flange and the bottom of the toilet is not caulked. The wax ring may be directing the waste into the pipe without leaking, but it may not be making an air tight seal.

Just a wild idea.

Have your plumber do a smoke test.

It will pinpoint with certainty where the sewer gas is entering the house.

I also have the same issue, i have 4 bathrooms and the smell could come from either one of then on no specific order. i have to keep the fan for times to get rid of the smell.

I checked the vent on the roof and they seem to be Okay. The wax have been replaced a few times as well.

I checked the vent on the roof and they seem to be Okay

How did you check it?

I went on the roof and looked to see if they are plugged it not.

They could be plugged way down inside. A quick visual inspection will only tell you if there's a bird's nest or something near the vent entrance.

Time to hire a plumber to investigate.

my plummer is suggesting is with the design of the toilet while he replace the gasket two times on each toilet. I have heard of the smoke test any idea what that is?

Get a different plumber. One who is willing to investigate instead of just replacing the same part over and over again and hoping for a different result.

Google 'plumbing smoke test'.