You have a BEE SPACE problem. The frames were spaced too far apart BY YOU.
"Bee
Space" was discovered or defined FIRST by Dr. Langstroth in 1851; and he
found that bees will build comb in any space greater than 3/8" or less than
1/4".  Hence, we
beekeepers think of it as 5/16", or the middle between 1/4" and 3/8".  Bees
will not build in their "bee space" using it as there "roadways" to get to
and from inside the hive.

Did you start your colony on 10 frames of foundation, or only 9?  Have you
mixed
frames of foundation with frames of drawn comb?  Are you using a factory made
inner cover or improperly designed homemade?

Are you feeding sugar syrup to this new colony?

Here is how things SHOULD BE STARTED:
1) ALWAYS put bees on 10 frames of foundation in one hive body, never 9.
2) Never mix frames of foundation with drawn comb frames or empty frames.
3) Properly designed inner covers have a "set-back" surface so the space
between
the tops of frames and the inner cover does not violate "bee space", i. e.,
leaves a space not less than 1/4" or larger than 3/8".
4) Bees tend to do strange things in comb building if there is a sporadic
nectar flow
or a dearth; or if it is too chilly and not enough bees to warm a larger
area.  Hence,
a beekeeper should feed 1:1 sugar syrup CONTINUOUSLY from the day the hive was
started until the colony has at least 20 frames drawn, and this may require
continuous feeding until September depending on the nectar situation in your
area.
Like an insurance policy, for over 60 years, I have always fed a new colony
that is on foundation from its start in April until September, and I have
never failed to have one of these colonies get through the winter with great
strength for next year.

George Imirie
EAS Certified Master Beekeeper
Starting my 69th year of beekeeping in Maryland