Assigning VLANs to the IST
Caution should be taken when assigning VLANs to the Internal Spanning Tree instance as it runs across every link to deliver the BPDUs regardless of the VLAN configured on it.
This can mean that a VLAN access port may become blocked if assigned to the Internal Spanning Tree VLAN rather than it’s own instance
The best way around this is to ensure VLANs are not assigned to the IST instance in Multiple Spanning Tree.
Trunk Link Pruning
A similar situation can occur when pruning VLANs off trunks, only prune all the VLANs in the same instance for a trunk link to avoid VLANs on trunks being blocked off.