Dyche, who has thrown his support behind the Video Assistant Referee system that was used at the World Cup last year and will likely be introduced in the Premier League next season, was left perplexed after a penalty awarded to his side was overturned.
Czech striker Matej Vydra was bundled over in the area in the first half leading referee Simon Hooper to point to the spot. As Vydra began his run-up to take the kick, however, Hooper signalled that the decision had been reversed by VAR.
"I am a big fan of the concept (VAR), but for the first penalty I felt the time to get to the decision was the big thing," Dyche told reporters.
"The referee allowed the set-up for a penalty and I know we are learning about it, but I think the referee should grab the ball and walk outside the penalty area, so there are no implications.
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"If it is a long decision, for me he has to move outside the box and stand there because Matej had got to the point of his run-up before the referee blew his whistle and said 'no'."
"That delay was what annoyed me, not the outcome because once you know that is right you quickly move on," added Dyche whose side were awarded a stoppage-time penalty that Chris Wood converted to put the Clarets into the fourth round.
"The timing was strange, and the outcome has to be made clearer because people weren't sure whether it was a penalty or not."
Selected FA Cup third-round ties were using the VAR system on Saturday and Premier League clubs have agreed in principle to introduce it from the start of next season.
UEFA will fast-track the implementation of VAR for the Champions League knockout stages this season.
(Reporting by Martyn Herman; Editing by Toby Davis)
