i have trouble sometimes with my civic, when i make a complete stop. first gear doesn't go in as easy. i have a stock 99 civic with d16y8

 

Check the MTF level.

 

Does it do the same thing when the engine is not running?

If it does not, I would look at the clutch release hydraulics, there may be a leak or a bypass in the system. Or you may have a pilot bearing that is hanging up.

If it does still argue, there may be another issue. definitely check the trans fluid either way...