As described, yes, it will cause major problems.
To use concurrent parallel/redundant links, other protocols come into play, or you will have created a bridge loop ... which has the potential (and usually does) swamp the switch with broadcasts and take everything down (occasionally requires a power-cycle to recover).
If you want to do "teaming" you need to set up the client and switch to use the same teaming protocols.
Teaming is usually implemented for two general functions; redundant/backup links or/and bandwidth increases.
What are / were you trying to accomplish?
As far as troubleshooting goes, if you don't have labeled cable runs, it can be ugly. Ultimately the quickest easiest to way is to unplug everything, and then start plugging things back in one link at a time, wait for the link to come up and watch the utilization indicators on the switch ... it it goes from blink...blink ... blink to solid all lights on within a few seconds, you have a redundant link, leave it out.
There are other ways, this is the fastest.
Your best bet is to hire a professional network person / consultant / VAR out to scope you network and make some educated recommendations ... then hire a Hitman to smoke the person that set up the original network and the person that hired 'em. This is what "getting off cheap" does for you ... a professional will walk away rather than set it up poorly (like this) because of unrealistic budgetary constraints.
