The conflict means that the file was changed in both source folder and target folder since the last sync.
For example, there is a file, MyFile.txt, in source and target and you need to keep the two files in sync. Normally, you modify MyFile.txt in source folder then synchronize it to target folder; Or, you modify MyFile.txt in target folder then synchronize it to source folder. In both cases, the source and target folder will contain the same and newest copy of MyFile.txt. There is no problem.
But the conflict will occur if you changed the MyFile.txt in both source and target. In this case, Beyond Sync can't know which change should be dropped. As default, Beyond Sync will skip these items. You can change the setting to "Copy to target", "copy to source" or "overwite old file".