We would need to see the configuration and some debugs, because what you're describing is not expected.
Here's the warning you will receive in CLI if you set the SSL-VPN port to be the same as the admin GUI port:
fgt (settings) # set port 443
Warning: SSL-VPN is using the same port number as administrative HTTPS GUI access.
If both are set to 443 and you have enabled port-precedence in the SSL-VPN settings, you may have issues connecting to the administrative HTTPS GUI access. To resolve this, you may change the administrative HTTPS GUI port or the SSL-VPN port.
[ corrections always welcome ]