Have your accountant writing to them and explaining is a good start.

Was the 2015/16 return filed late in fact?

I wouldn’t trust HMRC with a bargepole tbh.  As likely to be an error on their part as anything.  

Just like the Australian Taxation Office then Kimmy. Absolute fecking time sappers. Except the one time they called me about a mistake they'd made before my accountant and I even spotted it, resulting in a large sum of money coming back to me. That was a good day.

Have you moved house recently? I was fined £4K for a similar thing, turns out they’d been sending letters to my old address despite me telling them I’d moved because the different parts of the HMRC didn’t talk to each other. 

First appeal failed. They insisted they’d sent letters to my new address, so I was lying when I said I didn’t get them. Then I went into the “Gateway” on their website, found a letter from them to my old address, showing they were lying and/or incompetent. Appeal number two, with the letter as evidence, succeeded and I got my money back.

HMRC are a useless bunch of khunts; I had written to them five times to tell them I was not married (including changing requesting to change my details online), before they updated the information on the self-assessment portal.  Yet the letters I receive in the post state "Mrs".  I am now married, but I still use my maiden name for work and therefore do not use "Mrs".   

I am also considering submitting a subject access request to them and also HMCS who supposedly obtained my details from the electoral roll for a jury duty summons sent to my old address and which I received a week ago, yet I've been registered to vote at my new address for over a year...

This is why I always file stuff well in advance of deadlines and will start on my tax return in the next few weeks.