Yup, it's a FAT32 limitation.
I highly recommend sticking to FAT32 and use NSP Splitter if you are installing NSPs since exFAT has a lot of problems when talking about homebrew (not loading stuff, install errors and even corruptions). The forum is filled with people having problems due to exFAT format.
If installing NSP, you can use USB or Wi Fi on Tinfoil/Goldleaf (from XorTroll) as well, which already splits the files while installing.
Good luck!