It is likely that Gmail is not causing this problem and that it is user error.
All other things being equal, if a user is receiving a reply that was not also received by the delegated account, the investigation should start in that user's sent items folder to see if it contains the original message for which the reply was received. You may wish to temporarily disable conversation view while investigating.
Perhaps emails to delegated accounts are at times CC'ed, BCC'ed, or rerouted by Google Workspace rules to these users, and they are accidentally replying to some messages from their own Gmail account instead of the delegated one, which would now make them the recipient of the next reply instead of the delegated account.
Example Scenario
A. Website form submission
- An email is sent by a company website form:
Message 1: sent by form
-----------------------
From: [email protected]
To: [email protected]
BCC: [email protected], [email protected],
[email protected], [email protected]
Subj: Request for info
- The email is replied to by [email protected] from their account instead of from the delegated account [email protected]:
Message 2: reply by staff 03 to Msg 1
-----------------------
From: [email protected]
To: [email protected]
Subj: Re: Request for info
- The prospect's reply goes to staff03:
Message 3: reply by prospect to Msg 2
-----------------------
From: [email protected]
To: [email protected]
Subj: Re: Re: Request for info
Any possible scenario that places a copy of a message sent to the delegated account in another user's inbox introduces the risk that the user will reply to their copy of the message.
On the flip side, any message received from the delegated account can have replies redirected to any other included addresses, one of the CC'ed addresses for example.
For that matter, a person replying to a message can click reply and then add or remove any address they desire regardless if already part of the thread.
To understand why you are seeing this behavior one would start by reviewing the headers from the message that was originally sent as well as those from the reply that was received.