What are "cognitive abilities" in the context of critical thinking, and how do they differ from virtues?

Mostly innate or naturally developed mental capacities (perception, memory, attention, reasoning…) that work reliably when "normally" formed — the raw machinery thinking runs on.

Cognitive abilities are the faculty-traits: capacities that are largely innate or naturally developed and that function reliably once normally formed. Examples:

• Perception (visual, auditory, tactile…)
• Memory (long- and short-term recall)
• Attention (focus, selective perception)
• Introspection (awareness of your own mental states)
• Intuition (fast, non-discursive insight)
• Language comprehension
• Empathic understanding (recognising others' emotions)
• Logical inference (deduction, induction, abduction as basic operations)
• Mathematical cognition and pattern recognition

The crucial contrast: these are given equipment, whereas epistemic virtues are acquired, cultivated dispositions. You don't earn good memory the way you earn open-mindedness — abilities are the hardware, virtues are the trained habits of using it well.