Do references count towards the word limit for Science Magazine?
If you want to get published, follow the guidelines for authors meticulously.

If you're not bothered about getting published, then you are free to reinterpret them as you wish.

But if you do want to get published, read the words, obey the words.

You've already given us the definitive link for authors. The guide says 2500 words including references. So that's your limit. Keep to it. Yes, it does include titles. References include titles.

It doesn't matter that published articles are longer: they've been through peer review and editing. Your article hasn't, yet.

So if you want to get published, follow the guidelines for authors meticulously.

If there's still any doubt in your mind, talk to the editor. Remember, you want the editor to treat you fairly, so treat them fairly, be polite, don't waste their time, and don't ask them things that are already explicit in the guide for authors.