I uploaded a preprint paper to Research Gate. Then I realized that it is not allowed for the Journal I submitted my paper. I removed the paper from RG, but it was around two days available. Will I have any problem with the publisher in case the paper is finally accepted?
While I think it unlikely that you will have a problem, that is up to the journal - assuming they even notice it.
Of course, if they use automated systems to scrape preprint information they might know. But you will also, likely, be asked if the paper is available elsewhere. Phrased like that you can honestly say no, but if the phrasing is different (has it ever been available...) then you will need to explain to them what happened.