The Reds - who had two goals ruled out for offside - were leading 1-0 in stoppage time when Andy Robertson was deemed by VAR to have fouled Danny Welbeck inside the box as he attempted to clear the ball. Pascal Gross took and converted the spot kick - Brighton's second of the game - to snatch a late equaliser and deny Liverpool all three points.
The decisions left the Liverpool camp - including Henderson - furious after the game, but the Reds skipper was cautious in his interview with BBC Sport, saying: "I can't really speak about it because I'll get myself in trouble. If they're offside, you do the line thing, then what can you do?
"The third one, I don't know, it's not a penalty. You can think I'm biased but if you ask four or five or their lads they will say the same thing. They said it walking off the pitch. You feel as though there are a lot of decisions that go against you but that decision for me today is baffling."
However, Henderson did go as far as to say that he would prefer the game to be played without VAR in its current state.
"I don't want to speak for anybody else but in my opinion I would [do away with VAR]. I just want to play football as normal," Henderson continued.
"I saw Kevin De Bruyne saying in an interview they have changed so many rules we don't know what they are anymore. That for me is a big problem. We are talking about instances all the time and not the football. In my opinion I would rather play without it, yeah."
Liverpool are currently second in the Premier League table, level on points with leaders Tottenham Hotspur.