What sort of capacitor is it: ceramic, tantalum, aluminium?
Most large value ceramic capacitors, in a small package, saturate at a relatively low voltage, compared to their ratings. This means that the capacitance drops, as the voltage increases. A 50V 10µF ceramic capacitor will not have a capacitance anywhere near 10µF at 50V, or even 30V, but at 3.3V, it'll definitely be 10µF. In other words, if it's ceramic, then I would definitely recommend using a 50V ceramic capacitor on a 3.3V rail.
If it's an aluminium electrolytic capacitor, then this isn't an issue, but a 50V part on a 3.3V rail wouldn't be a problem.
Tantalum capacitors have a tendency to smoke when used close to their voltage ratings, especially when subject to high current surges/ripple. Going for 50V is still overkill, but won't do any harm.