I would guess that the two filesystems have different block sizes. A block is a storage unit that allows for some abstraction by the filesystem for tracking allocation of space. A single block is the minimum unit of storage; a filesystem that uses 4K blocks will use a 4K block to store a 1K file. More small blocks require more disk space for metadata. The optimal block size will vary depending upon the typical file size, the total capacity of the storage media, and the filesystem used. Modern filesystems will choose a reasonable block size, given the latter two factors; a sysadmin may tweak the block size or chooseb a filesystem given her expectations for the use of the filesystem.
So, the two filesystems may have different block sizes because the disks are different sizes, or because the two different file systems have different schemes for optimizing block sizes, most likely because of different handling of metadata. The two files that didn't take up an extra 4K may have been just small enough to take up one less block each.