Do you have any knock out or knock down to be sure which band is your protein of interest? More than one band, using and antibody against an endogenous protein, could be due to inespecificity or to different isoforms detecteb by the same antibody.

1, Considering whether the antibody is specific,

2,whether the protein extraction buffer is sufficient, for example the SDS concentration    is too low. 

3, For Caspase 9, it's really hard to conclude, may be you can use positive and negative inducable samples,like add drugs to induce apoptosis. 

Hope the above can help you, good luck.

Regarding the first picture of Bcl-2, the upper band represents the phosphorylated BcL-2 and the lower band is non-phosphorylated BcL-2.