小石 also means 'small stone' or 'pebble', but is slightly more neutral and descriptive; 石ころ can sound more casual or dismissive.
Etymology
Compound of 石 (いし, 'stone') and ころ, a suffix meaning 'small round thing' or 'lump'. The exact origin of ころ is uncertain, but it appears in other words like ちびころ (small child) and いぬころ (puppy).