Photographs showed Luis Godinho ducking the objects before handing them to officials as he walked away from the pitchside monitor after ruling out a Braga goal against Sporting.
Sporting defender Jeremy Mathieu turned Ricardo Horta's cross into his own net in the 44th minute but, after consulting the monitor, the referee ruled there had been foul on Sporting winger Gelson Martins in the build-up.
Braga players protested angrily and replays suggested there was either no, or minimal, contact with Martins who fell dramatically and clutched his head.
Braga won the game 1-0 with a late goal by Raul Silva, although they again had to wait while the referee checked with the VAR system for a possible offside.
There was also controversy involving the VAR system, which will be used at this year's World Cup, in Benfica's 2-0 win over Vitoria Guimaraes.
Benfica's first goal was scored from a penalty awarded with the use of the pitchside monitor after Jardel's header hit Joao Aurelio's hand although there seemed no way the Vitoria player could have avoided contact.
"I ask myself how they give these penalties in Portugal," Guimaraes coach Jose Peseiro said. "I don't see how you can ask a player to jump high without getting impulse from his arms."
Benfica's win lifted them on to 71 points, one ahead of Porto who play Belenenses on Monday.
(Writing by Brian Homewood, editing by Ed Osmond)
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