Plot hole: If they assembled the wet bike on the submarine, they wouldn't be able to get it off as it would be too big to fit through the hatch.
Plot hole: The aliens provide coordinates for a place to make a rendezvous with humans but do not specify a time. It's possible they're monitoring and will arrive when they see enough humans gathering at Devil's Tower, but the humans seem to expect the aliens to come more or less exactly when they actually do, somehow.
Suggested correction: Scientists were prepared for the aliens and knew when and where they would arrive, as seen by the extensive complex built at Devil's Tower. However, as Claude Lacombe, the French scientist, speculates towards the end, hundreds of humans may have had the Devil's Tower image recently implanted in their minds, saying they were "invited" but never made the connection. Neery figured it out and was compelled to go there at that time. Neery was then allowed to join a group of trained volunteers that were already prepared to go on the ship, while the previous "abductees" were being returned to Earth.
The aliens had not given a time to meet. The scientists may be taking it on faith that the aliens will know that they've arrived at Devil's Tower and are ready, but the way the subject of timing is left unaddressed on screen feels like an oversight.
We don't know for certain if the scientists were given a specific time, but it appears they were, or at least a general window. The long-lost objects, like the ship and the military aircraft, suddenly showing up in the desert, is an indication the process has started. If humans were given the precise location where the alien ship would arrive (Devil's Tower), then, logically, the aliens would also communicate when. The scientists were communicating with the aliens using tonal sounds. Early on, the scientists received map coordinates through dish satellites as repeating pulses. They would likely receive time information the same way. As often happens in movies, this info may be something that got edited out of the film, causing an inconsistency.
This might be one of those edge cases. Under most circumstances I'd agree we could assume arrangements were made off-screen by virtue of the fact that the rendezvous occurs successfully in the first place; but in the context of this movie, in which any and all forms of contact with the aliens is treated as profound and significant, leaving it unaddressed (not even with a line of dialogue) comes off like a plot hole. I suppose we'll just have to let our fellow website readers decide.
Plot hole: If the vacuum is strong enough to suck up a hand grenade, why isn't it sucking up the ampules?