Wrong Storage Space in El Capitan
File Clearing

As user2277872 mentioned it's probably a good idea to get a disk analysis application to find out what's eating up your disk space. A few good applications to start with are DaisyDisk, OmniDiskSweeper and Disk Inventory X, each available here, here and here respectively.

If you find no big files cluttering up your space, here's another link covering some things that might be using up your disk space that you may have overlooked: http://www.howtogeek.com/184091/5-ways-to-free-up-disk-space-on-a-mac/



Partition Resizing

However, if your 43 available GBs are on your Windows partition, no amount of file deletion on the Mac partition is going to help. What you need to do is resize the partitions.

Disclaimer: it's always a good idea to make a backup. In theory, no data should get deleted but things can always go wrong. Grab an external HDD and image your system onto it, or at least copy your important files over.


Boot into Recovery (Cmd-R on startup) and open Disk Utility.
Select your parent drive for both your Mac and Windows partitions (assuming they're on the same physical disk).
Click the Partition button in the toolbar and resize accordingly. You may want to allocate about 80GB to Windows or more depending on how much you intend to use it.
Click Apply and reboot. You should be able to boot into your Windows partition now.