I am presuming you are giving the gear lever a positive shifting motion when changing gears.
If the gear lever is completely tight on the gear shift shaft and the toe of the lever does not touch the engine sidecover when changing up, you may have a worn roller shift lever or loose screws holding this mechanism in place. See the exploded view diagrams of the SHIFT CAM and SHIFT FORK with all part names and numbers on the link below.
Cheers!
http://www.cmsnl.com/yamaha-yz125m1-2000_model10887/partslist/
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