My research supervisors want to patent an idea I made and I get a minority part of the invention I entirely came up with a novel idea. I did all of the research indepently. Both my supervisors want to patent the idea now. It seems that I'm getting a smaller stake in the patent according to the filing papers (they didn't talk to me about this). I own 25%, they own 37.5% each.

I can't help to feel like I'm being swindled. The university is paying for patent costs. But, I came up with the idea entirely on my own. Also, this isn't related to my main research project. I just worked on it on the side - so they didn't have much contributions towards the overall idea [actually one of them had literally ZERO contribution to the original idea and just happened to be my supervisor at the time]. 

Should I say something or is this common?
You should read your university's intellectual property policy.  If this matter is important to you, you should also consult a lawyer.  

I think you are probably confusing the concepts of credit and ownership.  The inventors get credit for creating the invention, but the owners have the right to exploit the patent.  Most likely the university owns all of the patent and the inventors who are employees or students own none if it.  The university may assign a portion of any profits to the inventors as an incentive.  This would be entirely at the university's discretion, and would typically be described in a published policy.