If you start having to make excuses every combat as to why the perfect, system-supported tool for the job just happens not to work this time round, then you've got to ask yourself if you're using the right system.
You don't have to make excuses - you just have to remember that Mage has never been light on the modifiers. Some things that are easy to conceive of in terms of the dot-value of powers become rather difficult to pull off when you count up what's required to put them into practice.
Entropy or Matter to rot or destroy a ship's hull.
You have the issue that either the object is very large (an entire ship) or small (one piece of wood in the hull, so not so effective).
(Life could achieve the same effect by supercharging the woodworms).
You'd have to stretch a bit to make that one not vulgar.
The 'spark in the gunpowder' Forces gambit.
Handled above - either this is a small working (easy, but unlikely to have the desired result) or large (and therefore difficult)
Or, for that matter, using Forces to prevent any sparks at all on the other ship, rendering all their gunpowder weapons useless.
This one is more subtle and creative - and interestingly more likely to succeed, I'd think. While in theory the system allows for massive, cinematic effects, the practical matter is that the Universe
resists large changes, but tends to allow smaller ones.
Matter to turn gunpowder to sand (or merely wet it) would have the same effect.
Turning stuff they'd already verified was gunpowder into sand would be Vulgar. Transforming casks they'd not opened yet might not be, but they'll still get shots off with ready supplies. Wetting gunpowder would be simpler - but it would require creation of matter (water) which calls for higher sphere ratings than transmutation of matter. And, as Mage deals with patterns, you can't transform some of the gunpowder to wet the rest without making the working notably more difficult.
There's one simple question we are not addressing here - how advanced are these mages?
In M:tA rules, a starting mage has maybe Arete 3, and rolls a whole whopping 3 dice to work magic, and most magics need multiple successes to make effective. Most workings are difficult for these guys - they have to be rituals, or at least extended castings for several rounds to pull off. And, they probably have 3 dots in one sphere, 2 dots in a second, and one dot in a third sphere - they may not have the sphere combinations to pull most of these off to start.
More advanced magi are, of course, rather more terrifying
