word-by-word translation of こんな遅い時間に来られても困ります。
Here's the breakdown, first word by word.
"this kind of (something)"
"time", "time of day"
Locational / temporal particle: "at"
passive conjunctive form of 来【く】る
inclusive particle: "also", "even"
Polite conjugation of 困【こま】る: "to be stuck, to be in a pickle, to be in an unfortunate situation"
Putting the first half back together:
"this kind of late time at" → "at such a late time as this"
Putting the second half back together:
[PASSIVE] even [someone] is stuck" → "even if [he / she / you / it / they] come, [I'll] be in a bad situation"
Explaining the passive here involves an advanced topic -- the 来【こ】られて is an example of the "suffering passive". There are various posts on the Japanese Stack Exchange about this: see also https://japanese.stackexchange.com/search?q=suffering+passive
Broadly speaking, it's a bit like in English when someone says "they went and did XYZ on me". It implies a negative result.
Putting it all back together
"this kind of late time at [someone] comes
[PASSIVE] even [someone] is stuck"
"At this late hour, even if they come, it won't be good."
The implication is that 1) "they" were expected, but didn't show up, and 2) by this point, the speaker doesn't want them to show up.
Please comment if the above does not address your question.