First of all, feeling agony at any time is not ‘normal’. Whether or not you’re meditating, it really doesn’t make sense to make agony a normal reaction. Subtly, it happens when you’re a beginner at meditation, you suddenly feel a lot of restlessness before finishing your task. Or something stops you & you get up suddenly, without being able to control the restlessness. Let me tell you that this is very common in meditation. It’s very common to experience pain while meditating. It could be in the form of external pain,like imbalance in the body, muscular tension, or internallyby the release of several hormones altogether.
Just think about it, meditation is a new task that you’re setting your foot into. There are bound to be issues regarding basic adjustments for you. This could be caused by the release of mental tension. You are connecting so deeply with yourself for the first time ever. There are bound to be several changes. Thus, feeling agonized or non-harmonious is very common in meditation. Your body or mind isn’t habitual of sitting quietly for so long. Thus, it produces a rush of physical activity or emotions.
Remember that it is completely normal, and you just have to train your mind for doing it.
It sounds counter-intuitive to welcome pain in this way, but you'll find it much easier to work with if you do. So to begin with, try if you can to get comfortable just sitting with it - essentially making friends with the pain. Pay more attention to your reaction to the pain, rather than the pain itself - that's where the real insight is. Don't be too quick to make a judgment or assumption, but rather take the time to really investigate. If this investigative approach is done in the right way and with a natural curiosity, then it can really transform the way pain is experienced.