It may be best to formulate this with additional states. For example, for at most two consecutive 1s:
:- use_module(library(clpfd)).
at_most_two_consecutive_ones(Day) :-
automaton(Day,
[source(n),sink(n),sink(n1),sink(n2)],
[arc(n, 0, n),
arc(n, 1, n1),
arc(n1, 1, n2),
arc(n1, 0, n),
arc(n2, 1, false),
arc(n2, 0, n)
]).
Example queries:
?- at_most_two_consecutive_ones([0,0,0,1,1,1]).
false.
?- at_most_two_consecutive_ones([0,1,1,0,1,1]).
true.
?- at_most_two_consecutive_ones([0,1,1,0,1,0]).
true.
For a more general solution, you have to build an automaton on demand when given the maximal length of a run.