Misaligned floor joist hangers
Rather than jacking up the joists it may be easier to sister some 2x6's onto the sides of the floor joists where the mismatches are noticed. These could be wedged into place and then fastened into place on the joist sides. The better way to secure the sistered members will be to apply construction adhesive to the mating faces of the lumber and then securely nail them together. After the adhesive has dried it will be stronger than the nails themselves and will distribute the load into the joist in a uniform manner. 

Note that if you are aware of places where subfloor above has joints in wood pieces directly over the joist is would be a good idea to sister the extra member on both sides of the joist.