What's the difference between using and not using the little comma? I don't mean in pronunciation, but in meaning
Little comma? Do you mean the little tail (ogonek) that changes e into ę? This seems the most probable to me. Well, "piję" is "I [drink/am drinking]", while "pije" is "[he/she/it] [drinks/is drinking]".
It sounds like pije and mleko are meshed together in this spoken sentence. Is this common with many Slavic languages? Russian and Ukrainian seem to do the same thing.
It depends how fast someone speaks. In all languages words can meshed together in fast speech.
Well, I'm the native speaker and I agree with you. This thing is very common, especially in Russian, but you will get used to it provided you practice and listen to music or watch films