It is a mistake.
"Our end" [or "my end"] refers to someone's side of an arrangement, procedure, or sometimes a point of view. You might hear:
From our end, things look fine
There is no problem at our end.
"On" our end could possibly be correct in a context where you would normally say the problem is "on" something - for example when there is interference on a telephone call, there is said to be a problem "on the line", so in such a situation you perhaps might say "there is a problem on my end [of the call/line]".
"In our end" seems the most unlikely to be used correctly, and certainly does not sound correct in the context of your example, which should be "at":
We are unable to locate your order at our end.
This is because it speaks about locating something, and you would use "at" to denote a location.