Time Machine keeps track of files and folders that have changed since your last backup. If Time Machine loses track of files and folders that have changed since the last backup, it will compare an "inventory" of your current data to an inventory of your backup. When this happens, Time Machine displays a "Preparing..." status message for a longer period of time.
After the comparison is complete, Time Machine backs up new and changed files. Try not to interrupt Time Machine when it is "Preparing" or when it is backing up files because that could cause the next backup to take longer.
Depending on how large your data is and how large your backup is, and how fast the connection is to your backup disk, this "Preparing" process may take significantly more time.
If you use Anti-virus software
If you use third-party anti-virus scanning software and have issues, make sure your Time Machine back up folder (Backups.backupdb on the Time Machine disk) is excluded from virus scanning.
How can Time Machine "lose track" of changed files and folders?
Time Machine might lose track of files and folders that have changed if your Mac is not shut down properly, or if a mounted disk is not removed properly by ejecting it first.
This might also happen if you just installed a software update, or if you use your computer for several days without performing a Time Machine backup (by not having the disk connected, for example).