The problem comes up already with a "more minimal" example:
\documentclass{article} \usepackage{amsmath} \begin{document} $\breve{\breve{a}\breve{b}}$ \end{document}
which produces
! Undefined control sequence. \macc@adjust ->\dimen@ \macc@kerna \advance \dimen@ \macc@kernb \kern -\dimen@
thus showing that the problem is not only in the repetition of the symbol. It happens with all math accents defined in terms of \mathaccentV,
\hat \check \tilde \acute \grave \dot \ddot \bar \vec \mathring
because these accents work by looking if their argument contains another accented symbol, in order to stack precisely the accents. This requires doing some global definitions, but somehow, if the argument contains two of these accents, the mechanism fails.
The "repeated symbol" is contained in the macro \macc@nucleus: after $\tilde{\breve{X}$, it expands to X and this is why this symbol is repeated (but I've not digged much into the details), since the definition of \macc@nucleus is done via \gdef.
The amsmath documentation doesn't point out that only stacked accents on one symbols should be used and, actually, it's safe to put an accent on a subformula provided it doesn't contain accents.
Solution.
As the macros are quite complex and require global assignments, it seems quite difficult to do surgery on them, so a different approach is easier. Define
\newsavebox{\accentbox} \newcommand{\compositeaccents}[2]{% \sbox\accentbox{$#2$}#1{\usebox\accentbox}}
Now \breve{\breve{a}\breve{b}} can be changed into
\compositeaccents{\breve}{\breve{a}\breve{b}}
and all goes well. As one can see, the argument is typeset before applying the "global accent" and stored in a bin, over which we can safely put the "global accent".
Should one need such buildups also in superscripts or subscripts
\newcommand{\compositeaccentsX}[2]{% \let\accenttemp#1\mathpalette\docompositeaccents{#2}} \def\docompositeaccents#1#2{\compositeaccents\accenttemp{#1#2}}
and $A_{\compositeaccentsX{\breve}{\breve{a}\breve{b}}}$ will work. It's better to stick with the simpler command, as the "extended" one requires to typeset four times the same formula.
Curiously enough, the accents package shows a bug in situations like this one:
\documentclass{article} \usepackage{amsmath,accents} \begin{document} $\breve{\breve{a}\breve{b}}$ \end{document}
will give no error, but will eat up the "a".
Very nice 10000th question on TeX.SE!
\o/\breve{\tilde{X}} \vphantom{\breve{}}