The most common and most likely answer to this crossword clue is the 6 letter word CRUXES
I've seen this crossword clue in The Guardian
C
R
U
X
E
S
Buddy explains!

The straight part
We know that "baffling problems" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case baffling problems = cruxes.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does CRUXES mean?
CRUXES noun- The basic, central, or essential point or feature.
- The critical or transitional moment or issue, a turning point.
- A puzzle or difficulty.
- The hardest point of a climb.
- A cross on a coat of arms.