This is a three part verb: Call in on (someone) or Call in at (somewhere). I called in at the library on my way home. Why don''t you call in on Maria some time? This is the similar to 'drop in on' someone or 'drop in at' somewhere. And no, it wouldn't be confused with phoning, because 'call' in the sense of phoning has no preposition eg 'I called Maria', which sounds very different from 'I called in on Maria'.

There are two different ways to use "call in." 1.You can use it to mean to get someone to come over and do a job. For example: We had to call in an electrician to fix the wiring. 2.You can also use it to mean stop by and visit. If you use it this way, you also need the preposition "on." For example: I called in on Bob the other day when I was near his house. It's not used very often however. I hear "stop by" much more often in American English. A native speaker wouldn't get confused because if you were to call someone on the telephone then you would simply use "I called Bob the other day," rather than saying "called in on."