I was checking the Ordeals in game this morning after the new patch.  It looks like a lot of the achievments I've done are showing, and I'm able to collect the rewards.  However, there are tons of Ordeals that are listed as 0/1 and 0/100 etc, even though I've done those things dozens, hundreds or even thousands of times.  Am I missing something?

Yup, like apparently I have not customized all 6 classes nor gotten a ranged weapon to max... but I have. Aparently it thinks in the over 300 hours I have played and the over 150 missions it did give me the ordeal for (or whatever the total mission completions ordeal was) that I somehow had only killed each boss one time and had managed to never kill any majoris or even get the total kills one despite having the 41k kills achievement... I mean I guess it gives me something to do but man it sucks how much each of the new datavault cosmetics costs in data. You need to almost 100% the ordeals to get every datavault cosmetic... that is not cool.

Tento patch se mi nelíbí, protože hraju jako taktic a úplně zničím svůj build. Granade launcehr have only 1 ammo pack with nev rework and also scan DPS is worst. i think its huge nerf.

Its bugged for everyone, hoping for a quick fix

I guess it is this way so we don't get instant 60% complection after logging in the game.:D 

Also, does anyone know if challenges like: kill boxx Y X times, counts even if my teammate does it? 

You are definitely not missing anything. It is inconsistent and even more confusing when being added this late after the release. This feature should have been in the game from the start.

I was shocked when I saw this. It immediately turned me off from playing it, especially when I found out about the nerfs. Although I played all the previous patches, purposefully farming coins to open cosmetics. But now, when they ask me to do half the ordeals that I have already completed again... no thanks.