This is a common problem with rear derailleurs.
Make sure that your derailleur sprockets are in the same plane with the chain rings at each and every gear.
Start off by setting the second largest chain ring to the correct position. Do this by setting cable tension. Then change gear to second smallest chain ring and observe,
* If the derailleur sprockets are aligned correctly with the chain ring, then you do not have a bent derailleur. You can proceed to setting the limit screws for the two top and bottom gears and you are done.
* If the alignment is not correct after you change to the second smallest chain ring, then your derailleur is bent. Fix it first.
If you still have problems even if you have correct alignments,
* Check your derailleur manual for the correct adjustment of the B-screw. This screw adjusts the distance of the derailleur sprockets to the chain rings in the vertical direction.
* When changing gears to larger chain rings, reduce force on the pedals and hold your finger on the shift lever until the shift is successfully completed.