If your rear wheel is locked up in first and second gear with the engine running, this is not a good sign. Have you ever ran the bike without oil in the transmission? Every time I've seen this, the chain was thrown off the bike and it busted the cases. The oil leaked out of the cases and the transmission locks up. Generally, it locks in fifth gear but it could lock up in any or no gear.
Your problem sounds like something is wrong with the low gear-second gear "clutch gear". The clutch gear is gear that slides sideways on one of the transmission shafts to engage the proper gears. If the bike will roll when in neutral, these may be the only gears affected. If the bike will not roll when in neutral, your problem may be in countershaft. Either way, the transmission could be damaged.
Now, if you're talking about the rear wheel locking up if you try to push start the bike, this is because in low and second gear, there isn't enough mechanical advantage in the transmission to overcome the engine compression. Remember, you transferring torque through the transmission backwards when you try to push start the bike. Try starting the bike using third or fourth gear instead. Standing on the pegs and dropping onto the seat when you release the clutch helps.
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