1/ Mail now adds info to Contacts — Mail can now auto-detect additional information it finds in emails (extra email addresses, phone numbers and so on) and add them to your contacts in the Contacts app. But you can modify this behaviour, since some people resent the additional information arbitrarily being added to the address details they may carefully manage. Open Contacts’ Preferences, and under General you can turn off ‘Show contacts found in Mail’ (above). Your Mac will warn you that it’s about to remove data.
2/ Duplicated data in Contacts — Contacts has a few ways to address duplicated data; for example, you can click on the Card menu and choose Look for Duplicates to automatically do some cleanup, or you can select a couple of cards and combine them using Card>Merge Selected Cards.
3/ Dealing with extraneous accounts — Open Contacts, and make sure the Sidebar is turned on (press Command-1 or choose View> Show Groups). For most, having just one list syncing consistently across devices is ideal and leads to the least amount of confusion. Some people missing certain contacts on iPhone that they know are on their Macs have found their Mac syncing by default to a Google account that wasn’t configured on their iPhones. (I really am no fan of Google and Gmail – I never understand why people choose Gmail accounts when they can have much better, more secure and better-synching – and also free – iCloud accounts.)
4/ Which accounts are you syncing? Open System Preferences and under Internet Accounts, in that pane’s left-hand list, you can again tell which accounts have contact syncing turned on. Make a backup of your contacts (File>Export>Contacts Archive) then drag any contacts from accounts you don’t sync to the one you do.
Turning off syncing for a particular account doesn’t delete those contacts from where they live on the server, so you can always toggle the syncing back on if you find you’re missing something later.
5/ On iOS — After your Mac is cleaned up, check your iOS devices, too. Similarly, you can see which accounts are being allowed to sync contacts within Settings>Mail, Contacts, Calendars.
If you toggle off contacts syncing for all except that one default account you chose on your Mac, everything will be all nice and neat.