Its not 100% reliable, but its pretty close.
http://brickseek.com/target-inventory-checker
Wave 1
207-00-5001 - Mario
207-00-5002 - Pikachu
207-00-5003 - Link
207-00-5004 - Peach
207-00-5005 - Yoshi
207-00-5006 - Donkey Kong
207-00-5007 - Kirby
207-00-5008 - Villager
207-00-5009 - Fox
207-00-5010 - Samus
207-00-5011 - Marth
207-00-5012 - Wii Fit Trainer
Wave 2
207-00-5013 - Luigi
207-00-5014 - Zelda
207-00-5015 - Little Mac
207-00-5016 - Diddy Kong
207-00-5017 - Pit
207-00-5018 - Captain Falcon
Wave 3
207-00-5019 Toon Link
207-00-5020 Bowser
207-00-5021 Rosalin & Luma
207-00-5022 Mega Man
207-00-5023 Sonic
207-00-5024 Sheik
207-00-5025 King Dedede
207-00-5026 Ike
When this happen, ask them to check in the back, look if they are hidden in another isle, or check the returns area, normally the system is updated live, so if they are not there its either an error in the system or someone stole them or have them in hand.