Not exactly, but it may not matter at some programs.
If you trained in Anesthesia, your Initial Residency Period (IRP) is 4 years, as anesthesia has a PGY-1 (either a prelim or a CBY) followed by 3 years of core anesthesia training. So you get 4 full years of funding. Since you completed 3 years, you have one year left (this assumes that you're counting your PGY-1 in your statement "I used 3 years of funding").
Since IM is 3 years, you'll be short by 2 years of funding. However, this isn't as bad as it seems. Institutions are paid by Medicare for training residents. They get two different payments - DME (Direct) and IME (Indirect). Once any resident gets beyond their IRP, the institution gets 50% of the DME and 100% of the IME. The details are complicated, but in many institutions the IME is much bigger than the DME. Hence, "reduced" funding is often 80-85% of full funding. All fellowships are reimbursed at this lower rate -- so any program with fellows is already dealing with this.
In addition, all programs are capped at the maximum number of residents they get reimbursed for. Many programs are over this "cap", having decided that training more residents was a good decision anyway. In that case, any place that is over their cap isn't going to get paid anything for some number of their residents, and they could just put you in that group and then there would be no financial impact to them at all.
In summary, this can be a problem at smaller programs that are highly dependent on their CMS funding. Many larger programs will simply not care, it may make no difference at all or be a rounding error in their budgets. Last, all of this CMS money doesn't go to programs at all -- it goes to the institution. So in the end it makes little difference to a PD.
If you want to read all about GME funding, read the report here:
Medicare’ Payments for Graduate Medical Education: What Every Medical Student, Resident, and Advisor Needs to Know