There is a chance that this could be mint rust which is a fungi. This can over winter on the rhizomes or possibly in the soil as well.
The best solution is to dispose of your mint along with the soil and start again. Disinfect all pots that you have grown the mint in. If you are taking root cuttings each year, you can wash the rhizomes in hot water before planting them in new sterile soil each year. This will hopefully prevent the fungi from returning.
In the kitchen garden, I divide our mint plants each spring. The plants are then grown on in clean soil and pots. This keeps them healthy and prevents the need for cuttings.
I hope this helps.