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Can you ever out multiple units inside a fortification?

Some Forts - such as the Fortress of Redemption - are actually multiple buildings connected together, and you can have one unit in each "section" (plus attached IC's), plus some units occupying the battlements.

Other than that, you follow the rules for embarking into a transport vehicle, including the single unit restriction (super-heavy vehicles, and some special rules (Storm Raven) allow multiple units but those are explicitly added - I'm not aware of any "super-heavy fortifications").

There is something similar to a 'super-heavy fortification' but it doesn't change the number of units which can be embarked. This rule can be found in the Stronghold Assault supplement and is known as Massive Fortifications. While all it does is raises the Armor Value of the building to near indestructible levels and makes it a great deal harder to get 'building destroyed' results on the table, it is something to keep an eye out for if your opponent pops down one of these monstrosities.

I don't like these buildings as nothing should require Class-D or Strength 10 weapons just to be destroyed....

Space Marine units divided down into Combat Squads can embark in buildings with their sister squad. That's the only time you can do it to my knowledge.

I think you mean BROTHER squad. Pssh... "Sister" he says.