Hi!
ACI doesn't participate in the Spanning Tree process, but upon receiving a TCN, ACI flushes all Endpoints in the concerned EPG(s)..
So yes, reboots of an ESXi Server which is connected to a port on a Cat6509 which has no portfast configured can cause that..
But one reboot would only cause that two times, once the port goes down and once when the port comes back up.
I don't think one reboot of an ESXi has caused loss of connectivity severe enough to "feel" it..
Maybe one or more of such ports were flapping?
And yes, if that was indeed the root cause, setting portfast on the ports facing the ESXi will fix it.
Generally you should enable portfast on all ports facing endpoints that do not participate in Spanning Tree, also servers.
.. I mean outside of ACI of course.
Cisco Switches (non-ACI) sent STP TCNs every time a link changes, you are turning that of by setting concerned links to portfast enabled..
Only do that on ports facing endpoints of course!
Best regards
Juls