If your unit gets tasked, but your CoC isn't tracking it and hasn't notified you, what defense do you have if someone tries to punish you?

Message sent does not equal message received. THAT is the defense. If you don't get an acknowledgement, you haven't issued an order. Here's an illustration of that from Hitchhiker:

“But the plans were on display…”
“On display? I eventually had to go down to the cellar to find them.”
“That’s the display department.”
“With a flashlight.”
“Ah, well, the lights had probably gone.”
“So had the stairs.”
“But look, you found the notice, didn’t you?”
“Yes,” said Arthur, “yes I did. It was on display in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying ‘Beware of the Leopard.”

That said, like COL Cudworth is saying, if you had a duty to monitor whatever communications channel they used to transmit the order on Saturday, you're in the wrong, even if them actually using the channel on the weekend is rare.

I think the elements in your question are the possible key to your rebuttal.

First, the question needs a bit more context about why your higher would take anyone to task. From your wording, my assumptions are:
• The duty was not performed;
• The digital message was an email;
• The timestamp of the email is from an after-the-fact dive through the mailbox it was sent to after your unit received a "WTF!?" type of call from your higher headquarters.

Going with those assumptions:
• Was the message sent to your unit through the normal/official channels (whatever they may be via SOP) or was it sent through a nonstandard/unofficial route?
• Was the message sent to a 'group inbox' that is regularly checked or was it sent to an individual (aka 'single point of failure') that wasn't available (leave? out of communications?)
• If it was sent to an unavailable individual, did higher know that 'single point of failure' would be unavailable (i.e., they were notified that certain senior leadership was on leave or an out of office response was turned on)?

Obviously there was a screw-up somewhere between the decision by higher to task your unit and the tasking being accepted by your unit. It comes down to if the standard process was followed or not. If it was, what was the unanticipated glitch in the system?

Bottom line: Did higher do what they were supposed to do and did your unit do what they were supposed to do? If the answer is that they both did appropriate actions, then you have identified a shortfall in the process and it needs to be addressed, minus the finger pointing (for example, if it isn't standard for formal taskings to be acknowledge, then a tracking should be set up to ensure that "message sent" isn't mistaken for "message received").

However, IF the message was sent via the standard/official route, such as a group mailbox that on-duty personnel were supposed to be checking or the operations NCO's personal account, and the personnel at your unit didn't do what they were supposed to do (nobody checked the group mailbox ... the Operations NCO was on leave but nobody told the higher headquarters to send messages to someone else and/or the Ops NCO didn't turn on an out of office response) ... Throw yourself on the mercy of the court.