Evolution in action.

[RoadRunner79]

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Perhaps it would be more apparent in real time, but I didn't see them stop much at all.

Watch the video again from 0:49 until 0:53. Remember, this is a timelapse across 11 days, so 4 seconds in the video is several hours in real life. The bacteria were reproducing quickly before and after that point in the video. There's a clear moment (when they reach the antibiotic) when they just don't reproduce in that direction, until a mutation occurs (at 0:53).

What I seen could possibly be explained as a bottleneck, where most of the bacteria where not able to survive in the antibiotic, but some where.  Once they got through, then they where able to spread in the new medium and start reproduction again.

I think you're missing the point. The bacteria are all the same species at the beginning (the same strain) and none of the original strain were able to survive in the antibiotic. Bacteria reproduce by splitting themselves in half, making an almost identical copy of themselves, so unless these resistant bacteria were introduced externally somehow (which is certainly a possibility that I suspect they looked into / controlled for), they must have come from the original strain after several generations.

If the original strain was not resistant to the antibiotic, and some of the strain's descendants are, that means they evolved the ability to resist the antibiotic at some stage, through a mutation.

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You might also notice that in addition to the isolated left vs right side, that in each progression, there are multiple lines, that extend on each side, within roughly the same time period. The more I look at it, the more and more that unguided random mutations, seem unlikely as a cause. But again further testing would be required. It is by far a very cool video and experiment. The other thing to keep in mind also, is that in the real world, natural selection is not so neat and tidy and population genetics is normally a little more complicated.