I have "Missing" with quotes, because there's always the tradeoff between storage space/performance.
There were a number of tables that are missing PRIMARY and/or indexes. Running these against your database should fix them up.
I haven't used these for an extended period of time, but I believe the worst error you would be likely to run into is that it cannot apply the index if there is a repeated key (i.e. In human_manager_history, there is more than one record for the same Manager, Managing the same Team, in the same Year. Yes, the way OOTP works, this should not happen, but a database cares not about OOTP and how managers work, it's just looking at a bunch of numbers.)
I didn't use a PRIMARY on the players_at_bat_batting_stats table, because even it doesn't happen often, a batter could face a pitcher twice within the same inning.
Code:
ALTER TABLE `human_manager_history` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `human_manager_history_batting_stats` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `human_manager_history_fielding_stats_stats` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `human_manager_history_financials` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `human_manager_history_pitching_stats` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `human_manager_history_record` ADD PRIMARY KEY ( `human_manager_id` , `team_id` , `year` ) ;
ALTER TABLE `league_events` ADD PRIMARY KEY ( `league_id` , `start_date` , `type` ) ;
ALTER TABLE `league_history` ADD PRIMARY KEY ( `league_id` , `sub_league_id` , `year` ) ;
ALTER TABLE `league_history_all_star` ADD PRIMARY KEY ( `league_id` , `sub_league_id` , `year` , `all_star_pos` ) ;
ALTER TABLE `league_history_batting_stats` ADD PRIMARY KEY ( `year` , `league_id` ) ;
ALTER TABLE `league_history_fielding_stats` ADD PRIMARY KEY ( `year` , `league_id` , `sub_league_id` ) ;
ALTER TABLE `league_history_pitching_stats` ADD PRIMARY KEY ( `year` , `league_id` ) ;
ALTER TABLE `league_playoffs` ADD PRIMARY KEY ( `league_id` ) ;
ALTER TABLE `league_playoff_fixtures` ADD PRIMARY KEY ( `league_id` , `team_id0` , `team_id1` ) ;
ALTER TABLE `players_at_bat_batting_stats` ADD INDEX ( `player_id` ) ;
ALTER TABLE `players_at_bat_batting_stats` ADD INDEX ( `game_id` ) ;
ALTER TABLE `players_at_bat_batting_stats` ADD INDEX ( `opponent_player_id` ) ;
ALTER TABLE `players_at_bat_batting_stats` ADD INDEX ( `team_id` ) ;
ALTER TABLE `players_awards` ADD PRIMARY KEY ( `player_id` , `award_id` , `year` , `day` , `month` ) ;
ALTER TABLE `players_career_batting_stats` ADD PRIMARY KEY ( `player_id` , `year` , `team_id` , `split_id` ) ;
ALTER TABLE `players_career_fielding_stats` ADD PRIMARY KEY ( `player_id` , `year` , `team_id` , `split_id` , `position` ) ;
ALTER TABLE `players_career_pitching_stats` ADD PRIMARY KEY ( `player_id` , `year` , `team_id` , `split_id` ) ;
ALTER TABLE `players_game_batting` ADD PRIMARY KEY ( `player_id` , `year` , `team_id` , `game_id` ) ;
ALTER TABLE `players_game_pitching_stats` ADD PRIMARY KEY ( `player_id` , `year` , `team_id` , `game_id` ) ;
ALTER TABLE `players_individual_batting_stats` ADD PRIMARY KEY ( `player_id` , `opponent_id` ) ;
ALTER TABLE `players_league_leader` ADD PRIMARY KEY ( `player_id` , `sub_league_id` , `year` , `category` ) ;
ALTER TABLE `players_streak` ADD PRIMARY KEY ( `player_id` , `league_id` , `streak_id` , `started` ) ;