I’ve had this happen a few of time (I can’t remember though if it has happened since I upgraded to C6.5). I eventually tracked it down to two related causes. It happened after I’d shortened a MIDI track (either by dividing and deleting a bit of the track after the division or by deleting notes without changing the length of the track).
An orphaned NOTE ON (ie no NOTE OFF event associated with it). The note just continued to cypher until it happened to be played again (when the NOTE OFF associated with that event silenced it) or a transport Stop occured.
An orphaned SUSTAIN ON (ie the associated SUSTAIN OFF was accidently deleted). All the notes on the channel continued to play. Those with a natural decay (eg Guitar) eventually went silent but those with a natural sustain (eg Organ) kept playing until the transport was stopped.
In both cases editing back the missing event resolved the problem.
I’ve also seen it happen with imported MIDI tracks. Never had time to investigate what was causing it but identifying the rogue event and editing it out and back again resolved the problem there too.