We are experiencing the same issue. However, it is happening with our FortiAPs, and any other kinds of devices we plug into the switches. The infrastructure is quite bigger than yours, but the problem is the same. It seems to be random. Sometimes Port2, or 5, 8, whatever, goes down then up, then down, up, etc, with the critical fact that when this happens on a port where an AP is, it makes the AP goes down and you can imagine the problem, as we have to wait for 5-6 mins to get the WiFi service back.
The same, we have disable, enable, combined, prayed, anything you can imagine to try identify what is the root of the problem. Even if it is a Bug, we have trying to catch what we have to disable/enable to get it fixed, at least until Fortinet decides to make it work properly.
We still receive messages on the Switch logs pointing a STP issue despite it has been completely disable (at least that's what it shows, even though it could or definetly is still running behind scenes).
Our infrastructure is big but simple. Actually, we don't need at all the STP protocol as we only have one possible path to each network, and so it is impossible to have a loop risk or whatsoever. At this desperate/frustration stage, if we could erradicate/purge the entire trace of the STP protocol from the Fortigate, we would do it.
Finally, it is good to mention we are on the Top of the current OS versions (7.2.4 on the Fw, 7.2.3 on the Switches, and 7.2.3 if I remember well, on the FortiAPs). Today, there is no possible newer version to upgrade any device in the infrastructure.
We used to love Fortinet and have several buildings with it, but this last building, we bet all on them, Firewall, Switches, APs, Full Licenses, etc, and all the project has been just a terrible mess. Before, we used to combine some brands, Fortinet at the top of the network with the Firewall, then HP Aruba switches, and finally, Ubiquiti/Huawei/Cisco APs... More complex to manage, of course, but Smooooooth. Nothing to do with this mess... It is a shame, we have open a case directly with Fortinet, requested support from one of our sellers/providers, do everything you can imagine, and still strugling with this since 3-4 months ago. We are about to return or drop 26 Fortiswitches and go back to the Arubas and the normal and ordinary VLAN/Trunking/Tag configuration of all the life.
So please, if you finally discover anything, please let us know as we are completely lost with this situation. I promise you to reach a beer where you are.
Of course, if I do so, I will pass the info too.
Here the hardware involved to provide you with some more info:
Fortiswitches 424E-FPOE, 448E-FPOE, and 448E.