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Without looking at the trace it is difficult to see the problem. However, the filter mstp.frame_type ne 0 means "show packets where there is at least one field with the name mstp.frame_type that does not have the value 0". In other words, if there are multiple instances of mstp.frame_type in the packets and at least one of them does not have the value zero, the packet is still shows.

The filter not mstp.frame_type eq 0 might work better as it means "show all packets where there is not one field with the name mstp.frame_type that has the value 0".

Please also be aware that filtering is at the packet level, not at the PDU level, so if there are multiple PDU's in one packet, it might not be possible to create a filter that works exactly as you need.