[xelxebar]

I noticed that you have some file dependencies not encoded in the targets. Also, you might like reading up on Automatic Variables ($@, $^, $<, etc). Anyway, just for fun I tried rewriting your script in a way that should Just Work a little better.

    texfiles    = $(wildcard *.tex)

    figures_ink = figures/junction_occupations.pdf
    figures_py  = figures/overlaps_barplot.pdf        \
                  figures/transmission_comparison.pdf \
                  figures/wigner_distributions.pdf
    figures     = $(figures_ink) $(figures_py)


    main.pdf: main.tex $(texfiles) $(figures)
        pdflatex $<
        bibtex $(<:*.tex=*)
        pdflatex $<
        pdflatex $<

    figures/junction_occupations: %: %.hs
        ghc --make $^

    figures/junction_occupations.svg: figures/junction_occupations
        $< -w 800 -h 400 -o $@

    $(figures_ink): %.pdf: %.svg
        inkscape -D -A $@ $^

    $(figures_py): %.pdf: %.py
        python $^

    clean:
        rm *.log *.aux *.blg *.bbl *.dvi main.pdf