$A= \{\text{an aircraft is present}\}$
$B= \{\text{the radar generates an alarm}\}$
$B^c=\{\text{the radar does not generate an alarm}\}$
$P(\text{present, no detection})=P(A)P(B^c|A)=0.05 \times 0.01=0.0005$
$$\text{Using Bayes' rule:}$$
$$P(\text{present, no detection})=P(A)P(B^c|A)=P(A)\frac{P(B^c)P(A|B^c)}{P(A)}=P(B^c)P(A|B^c)= (0.05 \times 0.01+ 0.95 \times 0.90)(0.01 + 0.90)≈0.78$$
Clearly, that's not right. So what am I doing wrong?

Data:
To be found are:
Calculations:
$P(A^{\complement}\cap B)=P(B\mid A^{\complement})P(A^{\complement})=P(B\mid A^{\complement})(1-P(A))=0.10\times(1-0.05)$
$P(A\cap B^{\complement})=P(B^{\complement}\mid A)P(A)=(1-P(B\mid A))P(A)=(1-0.99)\times0.05$
The last sequence of equalities in your question cannot be recognized as an application of Bayes rule. It is not more than just stating that: $$P(A)P(B^{\complement}\mid A)=P(A\cap B^{\complement})=P(B^{\complement})P(A\mid B^{\complement})\tag1$$
We can also find: $$P(B^{\complement})=1-P(B)=1-[P(B\mid A)P(A)+P(B\mid A^{\complement})P(A^{\complement})]=$$$$1-[P(B\mid A)P(A)+P(B\mid A^{\complement})(1-P(A)]=$$$$1-[0.99\times0.05+0.10\times(1-0.05)]$$
And combining this with $(1)$ we can find $P(A\mid B^{\complement})=\frac{P(A\cap B^{\complement})}{P(B^{\complement})}$.
But actually there is no need for finding $P(B^{\complement})$ and $P(A\mid B^{\complement})$
It is not clear to me how you found your expressions for $P(B^{\complement})$ and $P(A\mid B^{\complement})$
edit:
Your calculation of $P(B^{\complement})$ is clear now and correct. Both answers match.