I put toilet lid down when flushing but after it has completely finished flushing i leave it up. can bacteria still get into air leaving it up after?

Not an issue: We do not worry about a toilet if it is functioning normally. If it is producing an upward or outward blast of water, then it's time for a plumber. In general, presume that all bathroom surfaces have bacteria, and that the normal flushing of a toilet does not increase the bacteria level in the toilet to a higher level of danger. Normal handwashing and normal bathroom cleaning is good enough.