I honestly dislike how the “ている” form is often taught as the progressive form. To be clear, this is a minor use compared to its more common use which is comparable to the perfect in English. I disagree with “came” as a translation as well and favor “has come” or simply “is in Japan right now”. The “〜ている” form actually has three uses:
- perfect: “ここに来ている” pretty much always means “Has come here.”
- progressive: “これを食べている” pretty much always means “Is eating this.”
- remaining: “きれいでいる” pretty much always means “To remain pretty.”
I would mostly simply advise beginners to pick whichever of the three makes sense in context since it's usually only one, but there are actually some rules regarding the verb, that is to say:
- Verbs whose action has a clear endpoint of completion pretty much always have the perfect sense. So “送っている” means “to have sent”, “結婚している” means “to be married” and “来ている” means “to have come”, but “歩いている” tends to mean “to be walking” since walking itself does not have a clear endpoint.
- Other active verb can have either meaning depending on context. “書いている” can mean both “to be writing” and “to have written” depending on context. Usually only one of them makes sense.
- Verbs that already describe a state and not an action pretty much always describe remaining in that state. “違っている” is quite similar to “違う” but has a more permanent nuance to it.
Note that I use “verb” fairly broadly here. One can consider adjectives “verbs” for this purpose. Also, the “〜ている” form of i-adjectives is formed as in “美しくいる” without the “〜て” but it's still called that way.
But really, as said, in practice as a beginner, first assume the “〜ている” form has the perfect meaning. Should that not make sense then assume the progressive meaning.
It should also be noted that Japanese, much like English, has many verbs that have “laid aside” their original perfect meaning and now simply describe the resulting state without the origin, similar to in English saying “I am civilized.”. This does not imply that someone or something recently did the civilizing, one could always have been that way, similar to “My arm is still attached.”, compare “My arm is still fastened.” which implies that someone or something recently did the fastening. “付いている” is quite similar it means “to be attached”. “入っている” does not mean “has entered” but “is inside” with no implication it actually recently entered anything.