As per Documentation if there is an AUTOINCREMENT column sqlite creates an internal table called sqlite_sequence. This table can't be dropped.

Using Drop() with the sqlite3 migration driver simply attempts do delete every table found in sqlite_master

This leads to the error "table sqlite_sequence may not be dropped" if AUTOINCREMENT fields are used and records created.
In general it might be best to ignore tables starting with sqlite_ since they can not be created using create table and probably don't need to be deleted. In case of sqlite_sequence sqlite will remove entries entries if the respective table is removed so there is no need for any cleanup either. That's probably the same for the sqlite_stat* tables created by ANALYZE and so on.

The query for the tables to be dropped could look like this:
SELECT name FROM sqlite_master WHERE type = 'table' and name not like 'sqlite_%';