Notts missed-out on a £32,000 windfall, before watching Torquay scoop the plum draw of Birmingham City at home.
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"I felt I made a few decent saves, but we went to Torquay to win and we didn't," said Pilkington.
"It was a big disappointment not to be in the hat for the Third Round draw."
The 31-year-old - who signed for the Magpies in the summer - was keen to turn the attention onto the league though, with Notts set for two away matches inside a week.
"We now have two massive games coming up away from home," said the goalkeeper.
"It is very important we get some points on the board ahead of the busy Christmas period.
"We have missed out on a potentially big cup tie, so now we must focus on League Two and getting up into the playoff spots."
Pilkington was a doubt for last Saturday's match with a hand injury, but delivered one of his best performances since signing for the club to stop the level of defeat reaching embarrasing proportions.