Yes, animals can see auras and energies. They are also sensitive to them so it is best to avoid absorbing energy near a pet. It may weaken it. Also because the more you advance the more energy you will be able to absorb in a breath.
In my experience, while meditating in my room small insects (such as passing gnats) often come and bother me. I haven't noticed if it also happens with Yoga, but when I work with energies it always happens if small insects are there and I increase the amount of energy a lot. Generally it is not a problem, but as I said, be careful of animals nearby.
It can be obstructive (there have been cases where I had to restrain myself from meditating because my cat was sleeping next to me in bed). But if you see it in a different light this might help you learn to manage your time better and understand the importance of having that free half hour to meditate that usually some people always try to find a good excuse not to have.