Learn Italian: Il costo è basso, solo che dobbiamo addestrare ogni animale. - The cost is low, the only thing is that we have to train every animal.

Even though it ends in che, solo che doesn't express doubt, emotion, or a hypothesis. It's a conversational connector used to state a factual limitation or a "catch" (like "the only thing is..." or "except that..."). Because it introduces a fact, it requires the indicative mood.

Could I use tranne che instead of solo che in this sentence?

Not naturally. Tranne che generally means "except for" when excluding a specific item from a group. Solo che, on the other hand, is perfect for introducing a whole new clause that acts as a complication, afterthought, or obstacle to the previous statement.

Why is the noun singular in ogni animale when we are talking about training multiple animals?

The adjective ogni (every/each) is invariable and is always followed by a singular noun in Italian, just like "every" in English. If you wanted to use a plural noun here, you would have to change the phrasing to tutti gli animali (all the animals).

Is addestrare the standard word for "to train" in all contexts?

No, addestrare is specifically used for training animals or for highly drill-based, repetitive human training (like military recruits). If you were talking about training employees for a corporate job, you would use formare, and for sports, you would use allenare.