Sweden at home, Denmark at work
Malmö is the Swedish end of a 15.9-kilometre crossing, and Copenhagen is on the other side. A student can land at Copenhagen's airport and take a train into Sweden, and a Malmö resident can work in Denmark. Either may give you a Danish +45 number as their WhatsApp contact, or swap between the two.
For billing this matters less than it seems. Meta charges by the recipient's country code, and it puts Sweden and Denmark in the same group on its rate card, so a utility template costs the same whether the Malmö customer's number starts +46 or +45. What changes is the language: a Danish colleague of your customer reads Danish, a Malmö shop owner reads Swedish, and the Indian engineer who lives in Västra Hamnen reads English.
Store the country code, the city and the language separately for each contact. A Malmö address on a +45 number is normal here, not a data error, and a template in the wrong one of three languages is the most common way to look careless on this side of the Öresund. The Denmark guide covers the Danish rules for the other half of the commute.