Sounds like something is out of sync to me and no, there is not a setting in the phone or ACD configuration that would/should impact this.
As Terbert mentioned, there are different status columns to look at. If an agent is not on an ACD call but is on a DN call, I would expect to see the In Call Status column show "Busy" and either the DN In or DN Out column show "Active." Now, if they did have an ACD call also or were in Not Ready, you could see something other than "Busy" in the In Call Status column - but not idle.
Status messaging between the PBX and the CCMS tell the CCMS whether an agent is idle and available for a call, or if the set is activated in some manner and thus not available. So, the question is whether this is a onsie-twosie occurrence, or all all phones showing that way. You may need to update your patches, or possibly restart your CCMS, or deacquire/reacquire or even rebuild a single phone.
That's my two cents, anyway.