Spanning Tree didn't stop a loop

[thrtnastrx2]

A loop was created betweeen switch A and switch B and this caused the entire netowrk to go down.  Both switches had STP enabled and switch A was the root.  Switch A and switch B were connected via one copper port on each switch.  What I found was that switch B was configured with the interconnect port in a trunk, and switch A was not.  

example

• switch A:
• vlan 1
• untagged 48

• switch B:
• trunk trk1 eth 48
• vlan 1
• untagged trk1

the loop was introduced between switch A and B on some other ports, say 5 and 6 which are configured as access ports but the loop was not detected.  Anyone know why this misconfiguration between the interconnect ports would cause this failure?