(background I was a physics and EE TA for quite a few years as an undergrad and grad)
First a question; was it clear to students that the assignments needed to be done solo? It's hardly uncommon for a few students to meet up for a study group to do homework, and in that case a joint effort to solve the problems will lead to those students having the same solution method, no copying involved. If there was not a clear requirement that the homework most be done without collaboration this should not be an issue. I would suggest speaking with the instructor who assigned the homework to determine that.
Second, in the case where cooperation is not allowed it doesn't matter who copied or who did the work, the rules were broken by both parties and both parties should receive no credit equally. However, I would again suggest a discussion with the instructor, a grader should not carry that responsibility.
My suggestion - grade the papers normally, then write a short note with your concerns meant for the instructor, paperclip that note and the two homework papers together put it at the top of the stack you are returning. If you speak to the instructor when returning the assignments, bring up the issue at that time, otherwise make sure your phone number is on the note so the instructor can call you and discuss it.
I HIGHLY recommend against trying to make any further determination of wrongdoing, or scoring the papers at all differently - that is the responsibility of the instructor.