I will be assuming that you are using the FAT/FAT32 filesystem here, since you mention this is a SD card. NTFS and exFAT behave similarly with regards to allocation units. Other filesystems might be different, but they aren't supported on Windows anyway.
If you have a lot of small files, this is certainly possible. Consider this:
Ok, now the minimum space taken is 50,000 * 32,000 = 1.6 GB (using SI prefixes, not binary, to simplify the maths). The space each file takes on the disk is always a multiple of the allocation unit size - and here we're assuming each file is actually small enough to fit within a single unit, with some (wasted) space left over.
If each file averaged 2 kB, you'd get about 100 MB total - but you're also wasting 15x that (30 kB per file) on average due to the allocation unit size.
In-depth explanation
Why does this happen? Well, the FAT32 filesystem needs to keep track of where each file is stored. If it were to keep a list of every single byte, the table (like an address book) would grow at the same speed as the data - and waste a lot of space. So what they do is use "allocation units", also known as the "cluster size". The volume is divided into these allocation units, and as far as the filesystem is concerned, they cannot be subdivided - those are the smallest blocks it can address. Much like you have a house number, but your postman doesn't care how many bedrooms you have or who lives in them.
So what happens if you have a very small file? Well, the filesystem doesn't care if the file is 0 kB, 2 kB or even 15 kB, it'll give it the least space it can - in the example above, that's 32 kB. Your file is only using a small amount of this space, and the rest is basically wasted, but still belongs to the file - much like a bedroom you leave unoccupied.
Why are there different allocation unit sizes? Well, it becomes a tradeoff between having a bigger table (address book, e.g. saying John owns a house at 123 Fake Street, 124 Fake Street, 666 Satan Lane, etc.), or more wasted space in each unit (house). If you have larger files, it makes more sense to use larger allocation units - because a file doesn't get a new unit (house) until all others are filled up. If you have lots of small files, well, you're going to have a big table (address book) anyway so may as well give them small units (houses).
Large allocation units, as a general rule, will waste a lot of space if you have lots of small files. There usually isn't a good reason to go above 4 kB for general use.
Fragmentation?
As for fragmentation, fragmentation shouldn't waste space in this manner. Large files may be fragmented, i.e. split up, into multiple allocation units, but each unit should be filled before the next one is started. Defragging might save a little space in the allocation tables, but this isn't your specific issue.
Possible solutions
As gladiator2345 suggested, your only real options at this point are to live with it or reformat with smaller allocation units.
Your card might be formatted in FAT16, which has a smaller limit on table size and therefore requires much larger allocation units in order to address a larger volume (with an upper limit of 2 GB with 32 kB allocation units). Source courtesy of Braiam. If that is the case, you should be able to safely format as FAT32 anyway.
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Related: What is the difference between size and size on disk?
– Ƭᴇcʜιᴇ007 – 2015-11-10T13:33:43.863I have found something : Question. Could this be my problem also?!
– vfsoraki – 2014-01-20T09:54:56.73010Hello thelastblack, and welcome to SuperUser. I edited your question to remove the part about defragmenting, since the two existing answers focus on the size/size on disk discrepancy and the Stack Exchange format works best when each question posted is about a single thing. You certainly can re-ask that as a separate question however, although I think that the answers you have received so far on this question show that defragmentation will not help you. (It also generally does no good on solid-state media.) Feel free to [edit] your question further if you feel I changed your intent in any way. – a CVn – 2014-01-20T10:08:04.570
1@MichaelKjörling Heh, I just edited in a minor discussion on fragmentation (got distracted a bit earlier) – Bob – 2014-01-20T10:13:40.960
21@MichaelKjörling Don't edit questions retroactively to fit answers. One of the answers addresses the fragmentation part of OP's question. Your edit needs to be rolled back to avoid confusion. – DanteTheEgregore – 2014-01-20T14:07:08.100
5@DanteTheEgregore If you are referring to Bob's answer, which indeed has been edited to also discuss the effects of fragmentation, then before jumping the gun, please check the edit histories and timestamps on that answer and the question. At the time of my edit, Bob's answer did not cover the issue of fragmentation at all. If the OP wants to do so, editing back in "will defragmenting the media help me with this?" should resolve any outstanding confusion, although I still feel that is better asked as a separate question; IMO the matter of the difference between the two values is unrelated. – a CVn – 2014-01-20T16:15:12.490
@Braiam Yes, it is FAT32 formatted. I have to reformat the disk. – vfsoraki – 2014-01-20T16:32:09.970
11Looks to me like this app is seriously badly programmed – consider filing a bug report. I'm by no means a professional programmer, but I once hacked something similar together in JavaME, and of course one of the problems I had to solve was how to store all those little map tiles efficiently (storage & access) in a container. I ended up using uncompressed zip files. – A. Donda – 2014-01-20T18:15:06.997