Brighton ran out 2-0 winners over Leeds at the Amex on Saturday, meaning the Seagulls have done a league double over the Whites and boss Graham Potter has got the better of Marcelo Bielsa twice this term.
Leeds turned in a poor display on the south coast as Brighton powered to all three points, further banishing any lingering relegation worries in the Premier League.
Brighton beat Leeds 1-0 at Elland Road in January and Whelan feels he knows why the Whites struggle with playing against Potter’s side.
“You know what it is? Sometimes when teams play three at the back we don’t know what to do.
“We saw it last season”, Whelan said after the match on BBC Radio Leeds.
“You isolate the centre-forward against three; it’s hard enough as it is against two.
“That’s where your wing-backs become more prominent in the game and more important in the game because of that space in behind the full-backs.
“How many times did we get the ball over the top of the full-backs? How many times did we bring a centre-half out of position to allow maybe Patrick Bamford to have a one v one with a centre-half?
“We didn’t do that.”
Leeds now have just four more Premier League games to play this season, with home clashes against Tottenham Hotspur and West Brom, while they will also take trips to Burnley and Southampton.