Hmmm...the only thing I can think of is to go into the Samsung Contacts app, Select "More" (top right), then "Settings", then "Contacts to display". If "All contacts" is selected, try choosing another option. For me, I just use "Google".
Alternatively, under "Contacts to display", you can select "Customized list" then the gear icon. In there, you can select which contact groups to display from each of your accounts. In my case, I see:
- SIM card
- Telegram
- Skype
- Google
- Messenger
- Samsung account
You will almost certainly see different items on your list. Regardless, just select each account one by one, then check or uncheck items/groups within each account as you wish to see if that fixes the problem.