Viruses are really damned small, and finding the right organism in an infected cell is anything but easy. Cells are full of all kinds of molecule-sized bits and pieces of shit. As of today, it is not even a certainty that the ebola virus has been positively identified, let alone properly categorized; there have been reports of over 250 mutation variants, any of which might be a mutated ebola virus, or maybe just another virus which might just have been present through the isolation process. Maybe just random bits of crap from a previous disease vector or vaccination injection. Nobody really knows for sure. It's pretty murky down there, and determining which organism causes what effects is a sloppy science, and it takes a huge amount of time and energy to even approximate answers.
Viruses are indeed really damned small, but not much else is true in this paragraph, which is mostly FUD. Nobody outside the ranks of medical conspiracy theorists doubts that the Ebola virus has been positively identified. We are about as certain of this are we are about the identity of, say, a tiger or an oak tree. Its genome has been completely sequenced many times. Yes, mutations have been found in viruses from the current epidemic that weren't found in previous outbreaks. There's nothing surprising about this - we see it every time the virus emerges from the animal reservoir and causes a new outbreak. There is no question of this being just some 'random crap' or anything to do with vaccinations. The mutations occur at specific positions within the well-defined sequence of the viral genome, and if you are so inclined you can go along to the UCSC genome website and see exactly where they are: http://genome.ucsc.edu/cgi-bin...
The specific viral genes selected for insertion into the (adenovirus) vaccine vector weren't chosen at random - the Ebola virus has been studied for decades and there is a great deal of data on the functions of the proteins that its genes encode. Of course we can't know for sure if a new type of vaccine is safe and effective until it is actually tested, but this is a long way from just having some sort of vague hunch that it might be OK, as you seem to be suggesting.