Thomas was dismissed by the former international referee Fred Howard for elbowing the Saracens hooker, George Chuter, within nine minutes of coming on as a replacement.
Having viewed the match video, Saracens were also unhappy about two other challenges by Thomas, including the forearm tackle that put Kyran Bracken out of the match with a gashed cheek.
Saracens are not satisfied with the response from Swansea after making their concerns known to them and have applied to the English clubs' umbrella organisation, the English Rugby Partnership, for independent adjudication.
Swansea's team manager, Baden Evans, has requested a copy of the match video, which he should receive from Saracens tomorrow.
It is thought Evans was unwilling to add any further punishment to Thomas's sending-off. Swansea are due to take on Newport in the Swalec Cup at the weekend.
Neither the Rugby Football Union in England nor the Welsh Rugby Union have sanctioned the so-called "rebel" Anglo-Welsh friendlies. But earlier this season the RFU agreed to step in if an English player was subject to a disciplinary complaint, and it did so after the Bath prop, Victor Ubogu, was sent off against Cardiff in October.
Ubogu was spared further punishment. The WRU has not followed suit, however. "This shows the weakness of the disciplinary system for these matches," said Saracens' team manager, Mike Scott. "We are not happy with what we have seen on the video, and, if it was possible to cite the Swansea player for the challenge on Kyran Bracken, we would do so."
A copy of the match video has been sent to Howard, who did not see the alleged challenge by Thomas on Bracken.
Jonah Lomu, his fellow wing Joeli Vidiri and the No 8 Isitolo Maka have been dropped from the All Blacks training squad because they have failed to meet personal fitness targets, the New Zealand Rugby Football Union said yesterday.
The All Blacks' coach and convener of selectors, John Hart, said most of the 39 players had reached or surpassed their fitness targets over the summer.
"Fitness testing has shown that many of the players have achieved personal bests in both strength and endurance measures and it's a most encouraging start to a big year," he said.
But the three named players had failed to meet their targets and would not attend next week's camp, which will entail four gruelling days of military-style training. "We made it clear from the outset that if players did not meet certain standards they would not be part of the fitness camp, and we will not compromise," Hart said.
However, there was still an opportunity for all three players to prove themselves in the upcoming Super 12 competition, which pits 12 teams from New Zealand, Australia and South Africa against each other.
In this year's Super 12, Lomu will play for the Chiefs, Vidiri the Auckland Blues and Maka for South Island's Otago Highlanders.