Actually, you don't use "cum" at all, when you're speaking of a THING with which / by means of which you are doing the action.
"Cum", in that case, is actually incorrect.
This structure is called the ablative of means/instrument.
It's quite common with sentences like (please pardon the violence!): Milites gladio necat, "He kills soldiers with a sword " (< gladius, gladii, m., sword). Servum baculo verberat, "He beats the slave with a stick" (< baculum, baculi, n., stick).
in English the translation makes sense because water fills the cup means the cup is filled with water (by someone). But does this really make sense in Latin? The sentence sounds to me like it is saying water is actively filling the cup, as if water were an animate being that can fill cups (with something). This does not intuitively make sense to me. If so, the translation suggested by Suzanne would make more sense.
On the other hand, my question is, is Latin like English, where you can say this sentence this way to mean "water fills the cup" and have it mean the same thing as in English? Does this make any sense?
There are examples, in the Oxford Latin Dictionary, of subjects such as nomin. aqua , water, and sanguis , blood, used with the verb complere .
So Duolingo's "Water fills the cup" is okay.
Most of the examples, from what I can see, have people as subjects (sometimes as a crowd, turba ) filling up a place, or "filling" a place with noise.
I made some oil and garlic pasta for dinner the other night. Smothered in parmesan oregano, of course, with peas and cracked pepper. This, obviously, called for a nice dry Cantai. So I opened a bottle and poured myself a glass. It was wonderful, all inclusive. After dinner I thought I'd do a little surfing on the net and maybe a computer game or two. So I pored myself another glass and headed to the study. It was a long session, so I went back and got another glass. As the evening drew to a close, I thought, "Well, one more for the night." And I stumbled out onto the deck with a glass of wine for a smoke. Being a touch inebriated, however, I left the empty glass on the deck. It rained hard that night and in the morning, water had filled the cup. (My apologies for the past tense.)