Vulnerability to Sufficiently Powerful Magic
The Spectre can be injured or even slain by sufficient magic force, most notably the Spear of Destiny or a fully empowered Eclipso.
The Presence can impose limits on what the Spectre is able to do, as it did in binding the Spectre to a mortal host.
There are certain boundaries even the Spectre must not cross. If it does, it faces the punishment of the Presence. When the Spectre killed Nabu, it drew the Presence's attention, and was recalled.
Psychologically induced limitations
The Spectre is one of the most powerful magical forces in existence, but his power is dependent on his host for guidance. In the case of when the Spectre created a human form for Jim Corrigan, Corrigan wanted to rejoin humanity and unconsciously divided his power. This led to a situation in that if the two where not rejoined within 48 hours, Corrigan's spirit would have perished and the Spectre would have been left without a host.