Here's Deja Vu, the second Soviet mission from Yuri's Revenge, where you get to destroy the Chronosphere prototype (already built into the Chrono Miners, though). I won't even get that far to compare the tech used by the Allies with the one in the original Red Alert, but I've still got a question, though... How the hell Prism Towers got in there? I mean, even knowing how genial he is, Einstein wouldn't invent the Prism technology until he's done with the Chronosphere! Not to mention that, yes, he presents the said technology in the unexpanded Red Alert 2 to the player in person, as well as the ready-to-use Towers, but that's not until the fifth Allied mission. And Deja Vu takes (or may take) place just a bit after the First Soviet Occupation. And the Towers in this mission function just as their "official" RA2 counterparts.
I think you might be confused. In the stand alone game the Allied mission is to defend Einstein from the Soviets. Deja Vu is the same mission, except you are the Soviet forces. As for Einstein and his prism technology, given the Soviet threat this might be something he had kicking around and he was able to put into a weapon.
The vanilla mission in which Prism Towers are introduced is the first one in which the US could contact Einstein. Given the short time frame between Tanya blowing up the Soviet nuclear silos and Einstein's first appearance, it's likely Prism technology was already developed - It's just that the US could not get to use it yet without the Soviets nuking Europe.
Just like in the first Red Alert, the German border, as shown in the game, doesn't make any sense. What we see is the modern border which was formed in 1990. While it's reasonable that there is no GDR, as the division of Germany happened after the second world war, the country still lacks several regions in the east.
I know I'm thinking it way too hard, but... when General Carville is killed by the Crazy Ivan in the vanilla Allied campaign... how did the Crazy Ivan end up there? Especially when he was not being subtle at all.
I know it's a "given" that it was a Crazy Ivan who blew up Carville, but the Cuban Terrorist used to have the same Disguise ability as the Spy in the Alpha versions, so perhaps it was a Terrorist, who used his "disguise" ability to bypass security?