Well, for starters a lot of science works with models and models only represent certain aspects of reality that are useful for a given purpose.
Without being false or wrong, a model does not show you the full extent of "the truth" if there is such a thing.

For example we can describe all sorts of attributes of electromagnetic waves, but we cannot see the waves themselves, you cannot go and watch a magnetic field, you cannot touch and feel it, you cannot hear it etc., you can only study what it does to other things and how other things react to it etc. and then build a model around this.
And then even if you could sense it somehow, everything we sense is just an interpretation of our brain, certain stimuli that our brain receives and interpretes in a certain way, a bat for example "sees"/senses the world in a different way and has no problems with orientation in pitch black darkness where we are completely lost because our most important senses are "knocked out".
So everything science "proves" is only "proven" in relation to our perception of the world, it's possible that there are waves or whatever flying around the air and space that we will never discover and as such it's doubtful that science will ever "prove" everything.
And that's apart from what others said about science not proving anything in the first place.
I think science is more a way of us exploring our surroundings with the goal of manipulating them for our purposes and for that it is rather effective, so the goal is not to find some universal truth and prove it but to gain sufficient knowledge to attain certain goals that we have for ourselves, be it the survival of our race or just earning more money.

Just my thoughts for now.