Well I didn't think this could ever happen, and that any punishment would be achieved by docking points, but at least according to the table in Wikipedia some games resulted in both teams losing.
Summing the columns for wins and losses, you can see that 222 games were won, and 226 games lost. The total goal difference is also at -12.
For a head-to-head record I suggest using @Don_Biglia's suggestion and just listing the wins for each team, and the draws, for example as found here: http://www.statto.com/football/teams/head-to-head/manchester-city/manchester-united
If there is a match where both teams lost, then the match will not feature at all in the table.
The only drawback is that this could mislead somebody as the total number of matches played between the teams. Possibly a footnote could be added "data excludes game from DD.MM.2005 where both teams lost due to crowd violence"
The only other option I can think of would be to have four rows/columns: Team A Win / Team B Win / Draw / Other. But it would probably add much complexity just to cover one or two unusual cases.