"There were incidents, such as banned symbols, conflicts, refusals to obey orders, or attempts to leave the train," he said.
According to the spokesman, the only recorded violation was an attempt by a Nigerian woman to cross the border without the necessary documents. She was ordered out of the train.
Border guards stepped up security checks at the Kena and Kybartai checkpoints and Vilnius' railway station as fans traveled to the Baltic Sea exclave to watch a Nigeria-Croatia game and then back to mainland Russia.
Fan ID holders can travel free by train between the World Cup host cities.
Lithuanian border guards will also be put on alert as the 35,000-seat Kaliningrad Stadium will host Serbia vs Switzerland next Friday and Spain vs Morocco next Monday.