Hi Jimh
In reality the 90 days is only likely to be an issue if you do something that trips a switch. It is unlikely to affect any law abiding person. Otherwise, as Johnny Cash would say, they'd have to put half the town in jail.
In saying this, I am assuming you have an EU passport or would qualify for one.
Many people who regularly cross the border to France or Portugal keep the receipt for anything purchased, whether a café au lait or fuel for the car - or pay using a credit card which will show the merchant's name.
As far as I know, and I am open to correction, it is up to the authorities to demonstrate that you outstayed without good reason. I understand the EU governments are keen to come to an agreement with the UK.
If you are a UK passport holder and UK Prime Minister Boris Johnson carries out his threat to walk away if there is not enough progress on a deal, then the situation will be different and difficult for UK people who have lived in the EU for many years (also for EU people living in the UK). This concerns some 3 million people in total, so a lot is at stake.