this will not cause you any issues in it's self. it just means you never set the valves correctly. only checked the clearance of the tightest valve. not that a bike with 3k should need them doing. it's how I do a quick check on mine. to see if any of the valves are too close. when ever i take the top cover off. (usually it would be a exhaust valve).So I did a valve clearance check but I slipped the feeler gauges between the rocker arm and cam shaft. That was my first mistake I think.
no it's not the way to do them but it's not causing your present issues. by all means do them again properly once it's running.