Upvote:1
No, you should not have problems just because of that. Based on personal experience Spain border guards are quite lax on stamping passports (in violation of Schengen Borders Code, BTW), and their embassies know that.
Hold on your boarding pass and the evidence of your presence outside the Schengen area (some receipts etc), and present it to the embassy if you are challenged. Schengen embassies generally follow up with you if some extra paperwork is needed (again based on personal experience).