Flood water swept through Linen Green, near Dungannon. Several vehicles were damaged at a nearby Road Service depot.
Twenty four people were helped to safety as flooding affected parts of Northern Ireland.
Counties Tyrone, Londonderry and Fermanagh were worst affected, as Storm Desmond brought high winds and heavy rain on Saturday.
A number of roads remain closed due to flooding and fallen trees.
Gareth Bell, whose shoe shop was one of 31 units affected by flooding at the Linen Green complex, said there were "a lot of people in disbelief".
"As retailers, it's hard to fathom just how much it can ruin things over Christmas for everybody," he said.
Rivers Agency chief executive David Porter said the flooding was caused by a blocked culvert grille that caused the water to overflow.
He said the grille had been cleaned on Friday as part of weekly maintenance checks, but the sheer amount of rainfall brought down debris to block it.
"We were just hit by nature and a very significant rainstorm, although I would say that what we have seen, particularly in the west of the province, is a very good multi-agency approach to dealing with the flooding," he said.
The Fire and Rescue Service said it dealt with 31 flooding incidents. Most of those rescued were in vehicles that had become stranded in flood waters.
In one incident in Strabane, County Tyrone, 10 people were rescued from flooded properties at a housing development.
"We used ladders and inflatable rescue sleds to take them to safety, and other agencies have been involved in providing emergency accommodation," said Group Commander Andy Sinclair.
Assistant Chief Fire Officer Alan Walmsley said it had been a busy night for them.
"We started receiving our first calls for assistance to flooding incidents late in the afternoon, and those calls continued throughout the evening, spiking in the early hours of Sunday," he said.
A "high volume pumping team" worked for 13 hours in Lisnaskea, County Fermanagh, to "try and hold back flood water from impacting on the local community", he said.
He said the worst affected areas were "around the Strabane area, also Fintona and Enniskillen, and in the early hours it moved inward to around Cookstown".
In Clady, County Tyrone, an elderly man trapped by rising flood waters was rescued by a team that used a mechanical digger to reach him.
Gerard Foley, who lives in Clady, said on Sunday morning that the village was still badly affected by flooding.
"There are houses on the hill, and the rest is just water - Clady is a complete river," he said.
"You couldn't even pinpoint where the river is."
Road users have been warned about the risk of surface water flooding, as well as the risk of fallen trees or branches and other debris.
Stormont Environment Minister Mark H Durkan said households affected by flooding can apply to local councils for an emergency payment.
Mr Durkan said: "Individual householders will be eligible for a Â£1,000 payment as an offer of practical assistance to those who have suffered severe inconvenience, to ensure homes are made habitable as quickly as possible."
He added: "If you feel that you may be entitled to the payment, contact your local council as soon as possible and they will arrange for an urgent inspection of your property."
A shopping complex in County Tyrone has been flooded, causing stock damage thought to be worth millions of pounds.