The two being in the same train in Sweden or in Finland might not be out of the question, though. Savinkov arriving to Russia after Lenin could then be explained as him stopping/being held up on the Swedish-Finnish border or in Finland for a while, for some reason. We'd need some more details and clarification from the OP.
EDIT: Russian Wikipedia says Savinkov returned to Russia on April 9th, so that would be before Lenin arrived to St. Petersburg. So, further details are needed, methinks.
Judging by the following from Richard B. Spence, *Boris Savinkov: Renegade on the Left* (pp. 103-106) Savinkov returned to Russia by a different route than Lenin (ship from Britain to Bergen, then train to Finland) and arrived in Petrograd a few days later than Lenin:
"A few days later, Savinkov and other members of the Paris group participated in a defensist conference in Berne to discuss strategies for return. The meeting rejected the German route taken by Lenin and some other comrades. They opted instead to seek the help of British and French Governments.2 Boris took the opportunity to argue against any cooperation with "defeatists" like Chernov and Natanson, but the majority of the delegates refused to rule out collaboration.
"Savinkov was eventually among a select group of emigres granted Allied travel permits and visas for the trip home. An important consideration in the return of the emigrants was the dearth of passenger space on the convoys to the Russian Arctic ports. This imposed severe restrictions on the number who could travel at any one time, and created a keen competition for the available slots. Of course, it was also a convenient pretext to refuse transit to those emigres considered "politically unreliable." Furthermore, wives and children were deemed excess baggage, and it was virtually impossible to obtain visas for them. Thus, Savinkov was obliged to leave Evgeniia and Lev in France, a fact that may not have distressed him that deeply.3 Savinkov's outspoken support of the war and the Allied cause gave him an advantage in securing passage, and he was willing to help some others in their effort to return....
"The conversations aboard ship, and on the train that carried the returnees from Bergen to Finland, were not all nostalgic or amusing.11 There were heated political arguments, particularly over the war. The homebound emigres were divided into three main groups. First, and most numerous, were the defensists who believed that the war had to be pursued in conjunction with the Western Allies to a victorious conclusion. Opposed to these were the "Zimmerwaldists" who viewed the war as a criminal tragedy instigated by and fought for the benefit of the international capitalist cabal and the imperialist regimes they controlled. In between these two extremes were what Lebedev described as the "semi-Zimmerwaldists" who believed the war to be basically an imperialist venture, but who were also unwilling to see Russia lie down defenseless before the onslaught of a predatory Germany.12 Savinkov, of course, was a staunch proponent of the first position...He justified his pro-Allied stand not on his obvious cultural sympathies for the West, but on practical necessity. If Russia left the war, he argued, there could be only two possible outcomes: either Germany would win, and Russia would be at her mercy, or the Western Allies would be victorious without Russia and exclude the latter from any post-war settlement. Savinkov and his companions arrived in Petrograd (the renamed St. Petersburg) just before midnight on 21 April (new style) [I think this is where the confusion comes--the Russian Wikipedia was evidently using Old Style--DT.] 13 Because of the number of revolutionary celebrities on Savinkov's train, it was greeted by a wildly cheering throng of some 10,000. During the welcoming festivities, the name of Lenin, who had arrived only a few days earlier, was mentioned frequently and each time greeted with loud cheers. Boris was handed a copy of the Bolshevik leader's "April Theses" that called for a government based on the Soviets and an immediate end to the war. Savinkov determined then and there to combat such ideas by any means at his disposal..."
This just does not seem consistent with Savinkov and Lenin being on the same train. Also, there is no mention of Savinkov being on the train with Lenin in Spence or in either Michael Pearson's *The Sealed Train* or Catherine Merridale's recent *Lenin on the Train.* If it actually happened, you would think it would be striking enough for the authors to mention....