It may not be necessarily wrong.
To give two examples:
Farscape: Season 1. The episodes on DVD are in the same order as they were originally aired. The problem is, they don't make much sense in this order. So you constantly have to swap discs if you wish to watch it in an actual order.
Order on DVD:
1
4 (Throne for a Loss)
5
2 (I, E.T.)
3
7
8
9
10
11
13
12
14
15
16
17
18
19
20
21
22
Crichton is far to accustomed to all of the crazyness in Throne for a Loss and is then thrown back to WTH?! mode in I, E.T..
Leverage: Season 1. The episodes are in a different order than they were originally aired. And it works much better, because it didn't make much sense.
Order on DVD:
1
2
7
9
8
4
3 (The Two-Horse Job)
5
6
11
10
12
13
Again the episode The Two-Horse Job all these characters are already far to familiar with each other and then lose it again.