I have just come across an issue today where a 3rd party service desk for one of our clients is using FreshDesk and when they responded to our ticket INC-57335 with their reference [#INC-5974] in the subject line, this re-opened our ticket INC-5974 and attached the reply to the wrong ticket, which also meant the notification came to the wrong agent!
As more businesses adopt Freshdesk/Freshservice, this is likely to become more of an issue, especially for the MSPs.