You're not stupid, I'd feel the same way if I were you! Is there any way of taking a different med (for example same ingredients, different brand, not sure what that's called in English, or something that acts similarly)? It's pretty normal to try to avoid things you associate with somebody like your ex, and if there's the possibility to do so it's sometimes a good thing to just avoid it (therapists will say not always, but I don't think anyone would argue it's never a good option to avoid).
If there's no such opportunity and it's an important med, I'd personally try to first let myself feel whatever I feel and after that try to at least make the experience something that's different from the previous ones with the med. Say the ex took it at a certain time from a certain container, I'd maybe do a different time, different container, just make the situation as unique to myself as possible.