Did the scribes copy the letters correctly?

[ololololo]

This I find questionable.  If the text was written with isolated characters -- like Hebrew, Armenian, Cyrillic, Chinese, etc. -- the person would have to learn to distinguish the various glyphs of that alphabet anyway. Then he should just copy those characters as they were.

Depending on how the original as written, this is not always true. Horizontal lines could be barely visible or there could be extra connecting lines between the glyphs. The spaces could be uniform in within and between glyphs.

Here, "u", "n" and "ii" are very similar. There are connection lines between some glyphs so one could mistake i.e. "un" for "i□i" and thus invent a glyph "□" (square "o") that did not exist in the original.

There is well-known example of modern Cyrillic handwriting:

So, for the question "in a language that is normally written with isolated characters, are these characters always distinguishable for a person not knowing the language?" - the answer is definitely "no" for both modern and medieval writing.

The unusual "-aiin" - "aiiin" pattern everywhere could be simply explained if "ii" and "iii" are indeed parts of one glyph. Here in other thread there was a suggestion that this could be something like "ων". Here one can probably prove that the Scribe indeed has meant "iii" as three glyphs. But what if the Scribe himself did not know the difference?

About szynszyla... The example you gave is far from szynszyla (I speak as a person for whom Russian is his native language). The Cyrillic н is written without loops, so it should have been distinguishable. The example illustrates not a feature of the font, but a feature of the handwriting.
But it leads to the idea that I described in the post itself: the scribe could adapt the original alphabet to suit his convenience, so that at least it would be convenient to write with a pen, but in the process he could copy some letters incorrectly.