This exactly is happening to me as well. Makes it impossible to cast even the cheapest abilities even when I don't hold any index points.
There has also been another change in how energy pickups work in Index, I'm not sure if it's intended or not: previously it was possible to pick up several stacks in a single pass; presumably after an extended play without picking up any, they sort of accumulated, resulting in a big bump in your energy once picked up. Which meant that even with the constant energy drain (even when holding no points at all) it was still possible to cast at least a few abilities (like the aforementioned Iron Skin).
When both these issues are combined - which is the current state of Index - the remainder of the match must basically be done with no abilities whatsoever.