Are there historical instances of property rights not being respected/acknowledged between U.S. states, territories, and the federal government?

If I am not mistaken, drug laws are different in different states, which makes possession of marijuana (for example) legal in one state and illegal in another.

Also, federal government and local authorities could bar some kind of properties on places controlled by them. You would pass a metal detector and surrender any weapon you posses legally, when you enter court buildings.

In antebellum USA there where no metal detectors, but I can imagine that bringing weapons while visiting some US military installations (like arsenals) would be prohibited.

And also, some southern states established laws that made it illegal in these states to possess printed materials (books, magazine, etc.), that contain critique of slavery.

Ableman v. Booth, 62 U.S. 514 (1859), Wisconsin asserted their state's rights to not comply with the federal Fugitive Slave Act.

The Wisconsin Supreme Court in Booth unanimously declared the Fugitive Slave Act (which required northern states to return runaway slaves to their masters) unconstitutional. The U.S. Supreme Court overturned that decision but the Wisconsin Supreme Court refused to file the U.S. Court’s mandate upholding the fugitive slave law. That mandate has never been filed.1

There was a precedence in US history with the same issue of slavery. And polygamy on top:

The Utah War (1857–1858), also known as the the Mormon War:

At this time, the leadership of the LDS Church supported both slavery and polygamy or "plural marriage" as it was called by the Mormons. It is estimated that 20-25% of Latter-day Saints were members of polygamous households with the practice involving approximately one third of Mormon women who reached marriageable age.The LDS Church in territorial Utah viewed plural marriage as religious doctrine until 1890, when it was removed from the essential dogma of the Church by Wilford Woodruff.
However, the rest of American society rejected polygamy, and some commentators accused the Mormons of gross immorality. During the Presidential Election of 1856 a key plank of the newly formed Republican Party's platform was a pledge "to prohibit in the territories those twin relics of barbarism: polygamy and slavery." The Republicans associated the Democratic principle of popular sovereignty with the party's acceptance of polygamy in Utah, and turned this accusation into a formidable political weapon.
Popular sovereignty was the theoretical basis of the Compromise of 1850 and the Kansas-Nebraska Act of 1854. This concept was meant to remove the divisive issue of slavery in the Territories from national debate, allowing local decision making, and forestalling armed conflict between the North and South. But during the campaign, the Republican Party denounced the theory as protecting polygamy. Leading Democrats such as Stephen A. Douglas, formerly an ally of the Latter-day Saints, began to denounce Mormonism in order to save the concept of popular sovereignty for issues related to slavery. The Democrats believed that American attitudes toward polygamy had the potential of derailing the compromise on slavery. For the Democrats, attacks on Mormonism had the dual purpose of disentangling polygamy from popular sovereignty, and distracting the nation from the ongoing battles over slavery.

Although the term "war" might be a bit grave in light of the numbers of casualties, it also features some proper apocalyptic actions:

• 23 March 1858: Brigham Young implements a scorched earth policy. All faithful are ordered to move south to Provo and to prepare their homes in Salt Lake City for burning.
• 6 April 1858: James Buchanan: Proclamation on the Rebellion in Utah. ("a free pardon for the seditions and treasons heretofore by them committed;")
• 12 April 1858: The U.S. Army and Cumming arrive in Salt Lake City. Brigham Young surrenders the title of governor to Alfred Cumming.

Even in today's eyes it should be clear that marriage involves transfer of property rights. Now not any longer of the wife itself, but of her property. Whether a marriage is seen as legal or not has quite often numerous consequences regarding inheritance also.

The differences about territory, state and "wife ownership" did not really end after the war just mentioned.

The Church of Jesus Christ of Latter-Day Saints was incorporated February, 1851, by an act of assembly of the so-called State of Deseret, which was afterwards confirmed by act of the Territorial Legislature of Utah, the corporation being a religious one, and its property and fund, held for the religious and charitable objects of the society, a prominent object being the promotion and practice of polygamy, which was prohibited by the laws of the United States. Congress, in 1887, passed an act repealing the act of incorporation and abrogating the charter and directing legal proceedings for seizing its property and winding up its affairs.
(U.S. Supreme Court, Mormon Church v. United States, 136 U.S. 1 (1890))