That is perfectly normal for a 64-bit system. In theory, 64-bit programs go into the Program Files folder and 32-bit ones go into the Program Files (x86) folder. At least, that's the theory. It doesn't always work like this, but most of the time it does. In short, it doesn't really matter too much which of the directories a program is installed to, just accept the default that the installer wishes to use.
Programs File contains what are relevant to 64-bit.
Program File (x86) contains what are relevant to 32-bit.