There are probably no business types for which a Gibraltar-registered company would be a problem. But in some countries and for some types of business, a Gibraltar-registered company might lead to some minor inconveniences.
For example, if you are supplying products to Europe, your partners will have to explain why VAT is not included in the specification and delivery notes. However, this is more a matter of communication and different approaches to taxation in different European jurisdictions rather than a real problem.
It is more challenging to work in the countries where Gibraltar is still blacklisted as an offshore. For instance, if you open a Gibraltar company to supply Chinese goods to Russia, your cargo and documents will be examined at customs with additional meticulousness as Gibraltar is still on the blacklist of the Russian Ministry of Justice and the Federal Tax Service despite Gibraltar’s good business reputation in the rest of the world.