Sometimes you need to refresh the browser for actions to be updated. It's not a general problem however otherwise we'd have a lot on here complaining.
Next time you're adding for example 2d rt time take a note (screenshot) of the funds and the amount of rt time on your base(s) before you add it, then again afterwards. This will show if the funds are deducted. Refresh your browser and repeat the process of doing screenshots.
Once you have evidence of this happens check in Origin under purchases. They show use of funds in there. Again it should should be screenshot.
Once you have all your evidence (assuming it didn't register), then contact EA support for assistance.