Could you at least present one problem?

From the information about the YouTube video:
How is the significance calculated? See the video at minute 32; also, below is a breakdown regarding the significance software made by Professor Robert Haralick:

1. You enter into the software a group of words and skip intervals, and set how many runs it should do (the sample size).
2. The software finds the words it was given within a certain range of skip intervals according to what was actually found.
3. The software searches for the words in the Torah text and records all the places where they were found and with what skip.
4. After that, the software looks for the minimal-length passage that successfully contains all those words—using a fast algorithm created by Professor Haralick.
5. The software records the length of the shortest passage that contains all those words.
6. The software then randomly changes all the positions where it found those words, and then treats those positions as the positions of competing words—in other places. The software does not change the skip size, but changes the location randomly by means of a random number generator.
7. Then again the software searches for the minimal length of the passage containing those words after moving the competing locations.
8. Then again and again. In practice it did this 200,000,000 times. (By the way, there is a great piece of cleverness here by Professor Haralick: instead of changing the text and searching again, they use random repositioning and get the result in a fraction of the time the opposite method would take, while getting the same statistical picture.)
9. It compares the lengths of the passages with the real passage where the finding was located.
10. It checks: in how many runs was there a better success than in the original passage + half the cases in which there was the same success (if there were any such cases at all—and of course that is very rare).
11. The result over 200 million runs: 38 cases in which there was a better result for the 5 words. That is about 1 in 5,000,000 relative to the original passage (“there they shall call the peoples unto the mountain”).
12. “Israel” came out as 1 in 6,000 relative to the original passage (“there they shall call the peoples unto the mountain”).
13. “Moriah” came out as 1 in 30,000 relative to the original passage (“there they shall call the peoples unto the mountain”), and this was thinned out in order to lock the location and relate to it as though we had looked through all of Rashi’s commentaries, when in practice this thinning is much greater than what really should have been done.

I recommend the book Code of the Days of the World, which deciphered a completely new code in which every verse in the Torah corresponds to a year in world history (coming out to 6000 years), and in that specific verse what happened in that year is hinted at.

The number of words that can be found which yield some meaning is enormous. It seems like they first shot the arrow and then marked the target. So the sample here is not correct.
In addition, there are skips that supposedly prove Christianity. For example, a minimal skip of 3 in a chapter dealing with the priestly service of “the blood of Jesus his wife.”
There are also skips that lead to bizarre conclusions.
I don’t think one can rely on this.

Another problem that comes up is that it is not clear whether the version in our hands is the original text. There are quite a few differences between the text that the Sages had and the Masoretic text. Not to mention versions like Qumran, the Septuagint, and others.

No. The above-mentioned book has a chapter precisely about these questions.