If gears are difficult to select with the clutch pedal fully pressed, the clutch may not be releasing completely. Possible causes include hydraulic faults, cable or linkage problems, or damaged clutch and release components.
The transmission or shift mechanism may also be responsible. Whether the vehicle shifts normally with the engine off is a useful detail to share, but it does not establish the diagnosis by itself.
Do not force the shifter or keep grinding the gears. Contact Certified Transmission on 2112 West Broadway in Council Bluffs to have the concern checked.