@AKhan38 The behavior you're describing shouldn't be happening with native sequence behavior. The unenrollment criteria for sequences can be configured by Editing the sequence>Navigate to the automation tab.
Is it possible that users are booking meetings with sales reps or other users in the organization and that is triggering the unenrollment?
@AKhan38 I just tested this with my demo account and saw the same thing. Interesting that it unenrolls due to any email reply, I guess theoretically that makes sense as you wouldn't need the sequence to run any longer. I found this article that specifies:
By default, contacts will be automatically unenrolled when they reply to any email in the sequence or book a meeting on any scheduling page. These triggers cannot be turned off.
Maybe the solution here is to send these emails as marketing emails via a workflow instead, that would ensure delivery regardless of any other email activity that happens from other users.