>How often do you guys meet that bug?

Infrequently but sufficiently often to be quite concerned.

>When it will be fixed?

This bug has been reported on and discussed for years to the best of my knowledge without any fix or response from zos. Accordingly, I doubt it will ever be fixed. As @starkerealm has suggested document deposits you regard as important. If any of those don't register raise both a bug report and a support ticket, citing the former reference in the latter; said item(s) should be refunded/replaced by support. If there's an existing bug report in the bug section of the forum here then bump it with information about your loss; maybe with enough data zos may be more willing/able to address the issue.

As a possible workaround: when you make any 'important' deposits keep the guild bank interface open for as long as you can tolerate - maybe a minute as this seems to reduce incidence rate(caveat: this is anecdotal!). Guild bank interactions seem to have lower server priority than other stuff like making sure sorcs' pets remain flapping, leaping screen-hogs positioned for maximum obscuring annoyance, although it may just simply be a concurrency delay: multiple guild bank users interacting with the guild bank simultaneously. Currently, with the inability to see guild bank deposits of gold, it's impossible to verify deposits without pestering guild members who can see the guild deposit lists; I hope this, at least, gets adresssed.