What happened is that once it failed on "" it just skipped the first quote and moved on to the next character which was the closing quote so it matched on "," and continued from there. There are several ways to do what you want. Some are simple if you don't have to worry about embeded escaped quotes some thing like

/("[^"]*?")/g
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Would work.
If you have embeded escaped quotes you can use this:

/("(?:\\"|[^"])*?")/g
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like this

my $mm=qq(\"000.E+3\",\"\",\"\",\"\",\"QCA-086_2\",\"-1\",\"P\",\"FALS
+E\",\"this \\\"is\\\" quoted\"); 
my @p = ($mm=~m/("(?:\\"|[^"])*?")/g); 
print $mm, "\n", map {qq($_\n)} @p;

__OUTPUT__
"000.E+3","","","","QCA-086_2","-1","P","FALSE","this \"is\" quoted"
"000.E+3"
""
""
""
"QCA-086_2"
"-1"
"P"
"FALSE"
"this \"is\" quoted"
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There are several modules that you can use like Text::Balanced and Regexp::Common