On for example Sensei's Libray, if there is a picture of some stones and one is completely black, another one is white with a red circle in it, and then there are 1, 2, 3, 4, 5 and 6 with 1, 3 and 5 being black and the rest white, when were the stones without numbers played?

This example is under "Continuing in the corners" at senseis.xmp.net/?Joseki

My guess: first the black without number, then the white with a red circle, then the sequence.

I don't see the example you mentioned on the page you gave. That said, the 1-6 are the sequence you should care about once the extra stones have appeared on the board somehow. The implication is usually that you don't follow up with 1-6 right away, but save it for the endgame or some other point later on.

EDIT:
I think I found your page here... http://senseis.xmp.net/?BeginnersGuideToTheOpening

On this page, the black stone is the initial corner move, the white stone is the approach that breaks up the enclosure that is talked about a bit above there, and the numbered moves that follow are one possible joseki that continues from that point.

I guess you're referring to this: http://senseis.xmp.net/?BeginnersGuideToTheOpening#toc5

For any stones without number it is generally considered unimportant when and in what order they got there, unless there is a reference in the text, or perhaps a previous diagram, showing their order. And even then, their order is no longer relevant to the current diagram.

In the diagram you mentioned, the text mentions that prevented black from making an enclosure, so it is specified to have happened after the move at the 3-4 point. But if it had happened the other way around, i.e. was already present at the 4-5 point, and black played at 3-4 afterwards, the sequence through would still be equally valid in that position.

Markers like are used to be able to talk about specific stones or groups of stones in accompanying text without having to refer to coordinates, which are often consider clumsy.