Having a PvP set with the same runes as your PvE set causes the bonus counter to show up as 12/6. After testing it the runes all appear to function normally, so it’s just a display bug. The superior runes should be designated as different PvP versions to avoid any problems.
Sigils in general need better descriptions or bug fixes. I would suggest splitting them into two categories: main and offhand. Weapon swap and 30% 5 second cooldown sigils (such as intelligence and air) do not function together. If you swap your weapon, the proc sigil will not proc until and unknown internal cooldown expires. Conversely, swap sigils will not work until 5 seconds after a 30% sigil has procced.
5% sigils (such as +damage and +crit) do not appear to have any effect on the hero sheet. There is no way to confirm if they actually work, or to know that you can only use one of them at a time. Again, creating main vs offhand sigils will solve this problem.
Sigils of similar types (such as weapon swap effects) do not function at the same time. There is no tooltip or in game warning, or they are bugged.
Also, there needs to be some clarification on how the diving helm functions when it comes to runes, especially since it will cause your runes to show up as 7/6. I know it replaces your helm when you are swimming, but this can be confusing for many players. I would suggest making the diving helm a visual effect only and keeping your regular helm’s stats and runes active at all times.