A small number of lorries have faced delays at the new border control posts (BCPs) at Northern Ireland's ports.
BCPs are where food products entering Northern Ireland from Great Britain are being checked.
Several loads of food products arrived on Friday and Saturday without the correct paperwork.
Border officials worked with companies to retrospectively produce the necessary documents, though the process took more than 10 hours in some cases.
It involved getting the correct information from the firms in Great Britain that had sent the products.
This is being viewed as a specific timing issue related to the introduction of the new processes.
Some firms believed that if a consignment had begun its journey before the end of the Brexit transition period at 23:00 GMT on 31 December it did not need the new food safety paperwork.
However, officials from the Department of Agriculture, Environment and Rural Affairs (Daera) said what matters is the time at which the goods entered Northern Ireland.
Northern Ireland has remained a part of the EU's single market for goods while the rest of the UK has left.
This means that many food products from Great Britain now have to enter NI through BCPs.
These products also need health certificates, though some of the new certification processes will be phased in over the next three months.
NI's chief vet, who is in charge of the BCPs, has told the food industry it will not face penalties for non-compliance during the first week of the new system.
Speaking last month, Robert Huey said after that the approach to compliance would be toughened up.
Dr Huey said that in the unlikely event non-compliant goods were loaded onto a ferry and arrived in Northern Ireland they would either have to be sent back or destroyed.
"After day seven... if there's non-compliance the consignment will have to return to the exporter to get those issues sorted," he said.
"We will follow through on that, I have no option."