Is this new caulking you applied?
I'm thinking its "self-leveling" caulk, which is for flat surfaces, not vertical. On vertical surfaces you would want to use non-sag caulking.
You might be able to clean it off with mineral spririts, but I would not apply silicone caulk. Once applied, it cannot be caulked over if needed, because nothing will stick to it.
Jon
2016 Bullet 274BHS
2015 Silverado 1500 Double Cab
Andersen WDH