Why does western blot have so many unexpected bands?

The band pattern of a Western blot is determined by "technical" and "biological" reasons.

It is strongly influenced by the primary antibody: If you have an ideal antibody that has high affinity against a denatured/linear epitope and is thus very specific, you might expect only a single band. This is often not the case, so the antibody might bind unspecifically to other than your target protein on the membrane. Antibody dilution, intensify the washing, choice of membrane and blocking reagent can be optimised to decrease unspecific ab binding.

On the other hand splice variants/multiple isoforms of different molecular weight and degradation products of full-length protein (given that all of those contain the epitope that is recognised by the primary antibody) will result in multiple band on a western blot, even if your primary antibody is specific.

Here are a few possibilities:

1. Antibodies may not be purified. Monoclonal or affinition-purified antibodies are recommended. 

2. The concentration of primary antibody may be too high. 

3. For non-specific bands caused by secondary antibodies, it is suggested to only add secondary antibodies as control and exclude non-specific bands caused by secondary antibodies. 

4. Sample loading quantity may be too high. Set the gradient loading quantity, looking for the appropriate sample loading quantity, generally 20-50µg. 

5. Appropriately extend the washing time or blocking time. 

6. Protein samples may be degraded. It is suggested to use freshly prepared samples and protease inhibitors. 

7. The protein may be have post-translational modifications, polymers, isoform and so on.