You are wrong on so many levels. Over 60% of Utah land is owned by the federal government, and it is a similar ratio in most of the West. Grazing rights may be gained on private real property by a prescriptive easement or by adverse possession. It does not apply to government owned land (federal, state, municipal...). If Bundy was allowed to graze on federal land, it was because it was allowed (gov't chose to not stop it). Much of this land was acquired early in the history of the United States as a result of purchases, wars, or treaties made with foreign countries. The federal government used this land to encourage growth, settlement, and economic development.
The sheer fact that grazing rights were never codified for many years caused a plethora of range wars to start in the West. However, in 1934, the Taylor Grazing Act formally set out the federal government's powers and policy on grazing federal lands by establishing the Division of Grazing and procedures for issuing permits to graze federal lands for a fixed period of time. The Division of Grazing was renamed the US Grazing Service in 1939 and then merged in 1946 with the General Land Office to become the Bureau of Land Management, which along with the United States Forest Service oversees public lands grazing in 16 western states today. Some grazing land was homesteaded, but not much in the West. Today, the federal government employs principles of land use planning and environmental protection to preserve the natural resources and scenic beauty found on public land. The land in question is unequivocally owned by the federal government. Permits have been issued here before the BLM existed. And yes, it sucks if they aren't improving the land as they said they would, but it is public land, and I would HOPE the government charges a business to use it.
In regards to principles of ex post facto laws, you are wrong as well. Laws can always change, but they apply prospectively. Here is a hypothetical: lets say grazing on federal lands was legal for 50 years but illegalized today. If you kept grazing tomorrow, you would be breaking the law and subject to penalty. The fact is, the law was never codified before the Taylor act, but when it was first grazed by Bundy's family it was a federal territory, subject to their control. And permanent grazing rights were never established, that is a large part in what allowed two district courts to rule the cattle could be removed.
Basic constitution courses should be taught to everyone somewhere between middle and high school. It is so sad what so many people incorrectly believe regarding basic constitutional rights.