In the third line you have, after the alignment point,
{} \phantom{{}=} + (
(the first is automatically inserted) that makes four atoms
Ord Ord Bin Open
so this inserts spaces as
Ord (zero) Ord (\medmuskip) Bin (\medmuskip) Open
In the second line you have, instead
{} = + (
that produces the list of atoms
Ord Rel Bin Open
but the third atom doesn't make sense as a Bin, so it becomes Ord and the spacing is
Ord (\thickmuskip) Rel (\thickmuskip) Ord (zero) Open
Note that in the phantom you have “Ord (\thickmuskip) Rel” so this should explain the misalignments. In particular, the space between + and ( in the third line, that's not present in the second line.
Solution: a better phantom, with {} on either side, but embedded in a \mathopen, so the + will turn into an Ord like in the second line.
\documentclass{article}
\usepackage{amsmath}
\newcommand{\fakeeq}{\mathopen{\hphantom{{}={}}}}
\begin{document}
\begin{align}
f_\beta &= f_\beta \\
f_\beta &= + (-\Omega_{f_\beta})|_{(r, q)} \\
&\fakeeq + (-\Omega_{f_\beta})|_{(r, q)} \notag
\end{align}
\end{document}

Alternatively, don't make TeX into considering + as a unary symbol:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align}
f_\beta ={}& f_\beta \\
f_\beta ={}& + (-\Omega_{f_\beta})|_{(r, q)} \\
& + (-\Omega_{f_\beta})|_{(r, q)} \notag
\end{align}
\end{document}

In this case you may want to remove the \medmuskip on the left side of +:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align}
f_\beta ={}& f_\beta \\
f_\beta ={}& \mspace{-\medmuskip} + (-\Omega_{f_\beta})|_{(r, q)} \\
& \mspace{-\medmuskip} + (-\Omega_{f_\beta})|_{(r, q)} \notag
\end{align}
\end{document}

For a review of the spacing rules, see What's the right space to right the alignment of a right aligned align environment?
= {} &in the first row, and just&in the second. Basically you are align on the right of a relation, in which case care is needed to get=to use the correct spacing – daleif Apr 08 '16 at 16:00phantom-approach is better. Using your method wont align the=-signs – BillyJean Apr 08 '16 at 16:05+symbols, use&+instead of&=. – Mico Apr 08 '16 at 16:06={}&in the first two lines, and just&in the third one. – campa Apr 08 '16 at 16:09