I don't understand what's happening on either side, honestly - even as someone who pays fairly close attention, almost none of the reporting strikes me as reliable.
For example, this article is referencing another, published by "the Israeli-Palestinian outlet +972 Magazine". Right off the bat, I'm suspicious of their motives due to their location and its politics. The Guardian article couches statements as "reportedly" and gives an example of "[...] at least one case the unit misrepresented information [...]"
So I went to the source. It relies on unnamed sources. That's understandable, but this isn't an outlet that I'm familiar enough with to judge whether or not they're trustworthy.
The specific example the Guardian mentioned read like this in +972:
“They said: during the day he’s a journalist, at night he’s a platoon commander. Everyone was excited. But there was a chain of errors and corner-cutting.
“In the end, they realized he really was a journalist,” the source continued, and the journalist wasn’t targeted.
I... can't see anything to be upset about there. Israeli intelligence investigated someone, found insufficient evidence to believe they were guilty, and did not target that person. That sounds pretty reasonable to me.
This is not to say I trust pro-Israeli media, either. I don't. Articles I read there are similarly couched in "weasel words", making unsupported assertions and insinuations while carefully avoiding concrete statements.