They do agree on an awful lot of stuff, but the tools provided by the Bluetooth guys aged very poorly (i.e. their tools for generating GATT interfaces as C code is absolute garbage, full of holes and has a built-in buffer overflow capability).
The one thing nobody seems to do is stick to the standards provided, because they simply aren't broad enough for the creative stuff that people do with Bluetooth and Bluetooth LE. Most of us working in this space have some cack-handed way to advertise data without connecting because (for example) most of the connections to Bluetooth LE devices involve you having to do device discovery, even if you are connecting to 500 of the same damn device.
Also, the bluetooth library in Android started out terrible and didn't improve despite being replaced, the Bluetooth chips in most cheap phones are also rubbish and fail when you exceed their undocumented number of connections, often requiring a reboot of the device etc.
In short: You can sheet a lot of the problems back to an ill thought out spec and bluetooth chips in things like phones that just plain suck.
Things like RF interference - I just don't know. Sometimes there is just a heap more bluetooth traffic around than anybody knows about. Packet sniffers are relatively cheap, it's interesting to fire one up in a busy office and see how many bluetooth packet collisions there are (hint: it's a lot). Blame RF storms or whatever but it's more likely to be something advertising a lot and spamming the spectrum.