This situation can arise when YouTrack is configured to run behind a reverse proxy server. The proxy server can interfere with the process that keeps users logged in.
When users log into YouTrack, they are able to work with the application for a relatively short period of time (an hour or so), but are then shown a message that they have been logged out and are redirected to the login page.
Users can sign in again without having to re-enter their username and password, but they must repeat this process on a regular basis throughout the day.
The built-in Hub service uses a hidden inline frame to refresh authentication tokens. If you have set the value for the X-Frame-Options header to DENY for your reverse proxy server, users are logged out when their tokens expire.
Don't set X-Frame-Options header on reverse proxy level at all. YouTrack manages the header by itself to provide a reasonable level of data protection and to keep the application operational at the same time.
For more information, see X-Frame-Options.