Yes, you are correct! In this context, "poner" is used to convey the idea of "finding" or "encountering" problems with the documents. So your understanding is spot on!
If you have any more questions or need further clarification, feel free to ask.
¡Gracias y saludos!
Following on Silvia's explanation, we use the phrase "poner problemas", generally used in an impersonal way, i.e. using the "ellos" form of the verb poner. This is what you find in that sentence above. Other examples are:
Me pusieron muchos problemas al reservar una mesa para 15 personas porque el restaurante es muy pequeño.
I encountered problems (they gave me lots of problems, they resisted) when I booked a table for 15 people because the restaurant is very small.
Lleva una foto reciente para renovar tu pasaporte porque te pueden poner problemas; son muy estrictos con las fotos.
Take a recent photograph [with you] to renew your passport because you may encounter some problems (they may give you problems, they may say there's a problem); they're very strict about the photographs.
I hope that gives you a bit more context to understand that expression with "poner".
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