Learn English – Is it correct to say ” have been not” in English?

The placement of only in sentences is often a matter of contention.

Some speakers and writers don't care where they put it: they assume everyone will understand what they mean because they believe that everyone thinks and feels exactly the same way they do, a typically human presumption.

Other speakers and writers don't care because they believe that listeners and readers can read their minds: after all, they reason, I know what I mean! Everyone else will too.

Your sentences:

1 I have only been to London once before.

This is typical native-speaker English. All native speakers will understand it to mean I have been to London only once. The word before is superfluous unless you are now there a second time and uttering or writing this sentence. Notice, however, that I changed the position of the word only: I put it where it belongs, immediately before the word it modifies.

2 I have been to London twice only.

This is grammatical and idiomatic but somewhat rare. Normal syntax is either I have only been to London twice or I have been to London only twice. Because the word before is missing, there is no explicit implication that you are in London a third time when speaking or writing this sentence.

3 I have only been to London three times.

This is typical native-speaker English. All native speakers will understand it to mean I have been to London only three times. Your hope that the listener/reader will understand and assume that it means that you haven't been to foreign places other than London three times is misplaced: Native speakers don't pay attention to such things, only students of English grammar do.

Even the vast majority of professional linguists don't care where you put only because for them, as well as for native English-speakers, I've only been to London once equals I've been to London only once. Not for me, however.

But people who think and feel the way I do about where only belongs in any given sentence are shouted down and labeled peevish pedants or prescriptivists by the overwhelming majority of native speakers of English. But most people half a millennium ago told Christopher Columbus that he'd fall off the edge of the Earth if he sailed too far west, because they had a firmly fixed belief that the Earth was flat.

I don't bother arguing with people about this. I let them say and write what they want to say and write. The argument is a matter of faith; religious beliefs, like where only should be placed in any given sentence, should never be argued. I even sometimes say things like I've only been to London once (I can't help it: I'm a native speaker of English. I also sometimes speak Chinese-English because I hear and read it every day in Taiwan, so it seems quite normal to me, and I usually understand what it wants to say in idiomatic English), but I would always write it as I've been to London only once.

You can use have been when something has just recently ended. For instance, you would say:

I'm exhausted because I've been in meetings all day.

was would also be acceptable, but I don't think it's as common in this case.

But if it was in the more distant past, you must use was:

I didn't get any writing done yesterday because I was stuck in meetings all day.

It would be wrong to use have been here.