Happens on occasion. Rare, but not unheard of.
Yes it happens very occasionally. Only twice to me in over 2 years.
This can happen.
Say there are 1,001 alliances with 4 members to match in the war. There are 500 even matches, and the remaining team then would have to be matched to fight either a 3 or 5 member team. Assuming you can not leave any participating alliance unmatched I see no way to avoid this happening to someone whenever there is an odd number of alliances with the same number of participants to match.