The multimeter should measure the resistance between both nets (3v3 and GND) applying and small voltage and dividing voltage by current. As any capacitor is initially unloaded, you will always get an initiall short-circuit measurement, that progressively moves towards an open-circuit. I assume you mean that you are getting a continuous and prolonged short-circuit measurement. Is that correct?
If that is the case, then I see two options:
- You really have a damaged short-circuited capacitor
- There is something else in the board that is doing the short-circuit. It might be something broken, like a track, a via or a tin ball that don´t see anywhere.
In any case FvM advice to locate the short is great.