A late Luke Berry effort was not enough for Charlton to overturn an own goal and an Albie Morgan strike.
The second half was mired by a significant number of stoppages, which led to at least 12 minutes of injury time.
Jones believed that the amount of fouls awarded in the game was detrimental to the tie.
He said: “It became farcical. Every single time anyone came together it was a free-kick to Blackpool. There must have been 200 stoppages.
“The referee facilitated the way Blackpool wanted to play, he gave them a free-kick for absolutely everything.
“It absolutely ruined the game as a spectacle, it became 200 sporadic events.
“For me it was really frustrating, especially with that first-half performance because I thought Blackpool were excellent.
“We weren’t aggressive, we were passive, and in the second half we didn’t demonstrate enough quality.”
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