Pictures from the game show Neymar being held back by teammate Kylian Mbappe.
"The referee told me something he should not have - it was disrespectful", Neymar said after his side's Champions League game in Naples.
"I think it made sense to make a few changes, a few we had to make and a few we wanted to", said Klopp.
Kuipers and Neymar have history.
'He can not be as disrespectful as he was with me, ' Neymar added.
After initially awarding a penalty to Brazil, he informed Neymar that it was being overturned thanks to VAR technology due to a dive by the Brazilian star.
The run-in is the latest between the pair, who also clashed at the World Cup in Russian Federation this summer when Brazil were taking on Costa Rica.
PSG avoided defeat, which has to be considered a positive - the French champions are still alive in Group C and can harbour realistic hopes of finishing top.
While waiting to take a free, Neymar was booked in the 90th minute after he motioned towards the referee, seemingly unhappy at how close the Napoli players were.
Jose Callejon was offside when the ball was played to him before he was fouled by a combination of Gianluigi Buffon and Thiago Silva.
Napoli are top of Group C but level on six points with Liverpool, with PSG a point further back with two rounds of fixtures remaining.
Per ESPN, PSG chairman and CEO Nasser Al-Khelaifi also hit out at match-day officials when he claimed his side "lost two points because of refereeing errors".
"We'll have to battle until the very end, we're holding on tight", said Ancelotti.
Can Napoli do the unthinkable and upset the UEFA Champions League odds?
Cavani spent three years with Napoli, scoring more than 100 goals in all competitions before signing with PSG.