First, you should talk to her about these things. She may be getting closer to you, or it might just be something she likes to do. The only way to find out is to ask. This is a conversation you should have had either after the fact or the day after, but you can still ask now.
Second, eye contact can be a bit intense. It may have been too intimate a moment for you, which would explain your feelings of discomfort. Again, this is for you to sort out with her. If you're not comfortable with that level of intimacy then you should let her know.
Third, part of your discomfort may have been feeling like the relationship may be growing into something more emotional or intimate than what you're comfortable with. Maybe you're not into her in that way, or maybe you feel the relationship is moving along too fast, or maybe you're just not ready for a relationship right now. All of those things are valid feelings, but it's up to you to look inside yourself and sort things out.