It's definitely something you should talk to your instructor about if it is getting worse. You shouldn't feel like you have to sit that way to the point you are uncomfortable for days afterward. You should be able to sit comfortably.
Some questions about your situation: How long are you sitting in seiza in any gtiven class? Have you been sitting in sieza longer in subsequent classes? Or are you still sitting in seiza the same amount of time? It could be that because you are sitting in seiza for longer periods of time in class, it hurts more simply because you are sitting that way more.
I can't sit in seiza much past 10 minutes at a time at this point, even though I'm very flexible and have been training a year. But we're up off the mat so frequently in my dojo that there are few times in class where I'm in seiza more than 5 minutes at a time.
Stretching my calves and hamstrings helps me. Your instructor may have some suggestions for stretches.
Also, just sitting that way for a few minutes here and there outside of class to get used to the feeling has helped me. But only to the point where it just becomes uncomfortable, and certainly not to the point where it is painful.
Also, the first few months of aikido are painful. Especially if you are new to exercise, but even if you already have a good level of fitness, you will be working muscles you didn't know you have. This could just be some "delayed onset muscle soreness." Which can be as painful as anything.
Something else that may help you is to try to be observant of your body when you sit that way to try to find out "why" it hurts. Other than the obvious "I'm putting all the weight of my upper body on my feet and ankles."
For example, My husband, who trains with me, has huge difficulties sitting in seiza because of flexiblity issues and previous muscle development (was a fencer, has huuuge calves.
He pretty much balances his entire weight on his shins, and is unable to actually sit down. The fact that he's able to last as long as he does in that position is stunnig to me. If I had to sit like he does I could probably last 2, 3 minutes, tops.