Yes it's a safety feature. just stop botting for 24hours and you'll be good again.
1000 pokemons/ 24hours and 2000 pokestops. Else you probably teleported too far too quickly
Does Pokemon Go monitor activity individual account or by IP? I have three accounts running on the same Key and I believe that this stat is only monitoring total use within 24 hours regardless of which account was used, correct? (Is it safe then under that regard?)
Another thing too, is that if you use the same PF folder with multiple accounts it will not differentiate between the accounts and use the grand total, if you plan to use one key with multiple accounts (not at the same time obviously) I suggest creating multiple folders of PF for each account. This also allows for individual log files in the event one or two accounts are having issues but not all of the accounts.
Hope that helps.