I did two ops last night (friendship raid and the phoebe ops), managing to get 100 ops points in both. I was rewarded a Eldrid commander loot pack for both. When I went to open them, the animation was of a core loot pack opening. I received no faction gear at all from either loot pack opened, so I don’t think it was a visual bug.
Here is a video of this happening.
For what it is worth, I had previously completed the Phoebe operation with 100 ops points before. I had never completed the friendship raid with 100 ops points until last night. Both resulting commander packs turned into core loot packs.