When Miners find conflicting blocks that each build on the same chaintip, two or more competing chaintips emerge. At a certain point, a Miner will discover a new block that results in a clear elongation of one of the competing chaintips beyond the others resulting in the emergence of a clear longest proof of work chain.
At this point, any Miner working on a shorter chaintip will cease trying to build on the failed extension and migrate their work to the longest tip. Part of this process is the removal of transactions from the now defunct blocks and the construction and validation of the Merkle tree for the blocks in the new longest chaintip.
This is called a re-org, as it is the re-organisation of all transactions in the now orphaned chaintip, to match the ordering of the new longest proof of work chain.
These are common events (approximately one in every 300 blocks results in a race) and are an important part of the Nakamoto Consensus mechanism.