For the Edexcel English literature paper 1, we were asked to compare the poem Sonnet 116, and I compared it to "Prayer Before Birth." Can they be compared, and if not, will they give any marks if they thought it was the wrong comparison? Or will they look at what I wrote for the comparison?

Almost any two poems could be compared to one another, as almost any two poems will have something in common—whether that be an idea or a stylistic technique, a common characteristic between the speakers, or a similarity between the narrative structures. Generally speaking, as long as a student can give evidence and explain their comparisons, an examiner will not penalize the student. An examiner should not penalize a student simply because they disagree with the student's choice of poems but instead should reward the student for any comparisons that are evidenced and explained well.
There are plenty of good comparisons that might be made between Sonnet 116 and "Prayer Before Birth." Both poems, for example, are about the power of love. In "Prayer Before Birth," the speaker asks for a love which will protect and nurture her, whereas in Sonnet 116 the speaker declares that love has the power to guide one, figuratively, through storms.
One might also compare the language choices in both poems. For example, in "Prayer Before Birth," the speaker uses metaphorical language to express her fears that she will be oppressed: "with tall walls [that] wall me." In Sonnet 116, the speaker also uses metaphorical language when he says that love is "the star to every wand'ring bark." Both writers use metaphors to make their ideas more accessible.

Please don't worry—I used to examine this paper, and unless the rubric specifically tells you which two poems to compare, you are free to compare any two which you feel offer any material for comparison. I am sure you chose to compare these two poems for a reason and that you wrote some valuable things.
I probably wouldn't have chosen these poems as an obvious pair to discuss together, but I can see some areas of focus. You might have talked about, for example:
The tone and diction—how are they similar and different?
The rhyme scheme and form—whereas Sonnet 116 uses a very regular sonnet structure, MacNeice's poem is written in free verse, lent cohesion through the use of repetition.
Theme—they both, to a certain extent, focus on constancy and continuity, particularly the relationship between Time and humanity, within which Time obviously holds the dominant hand. They also both talk about love, although one focuses on a romantic love and the other on the love between parents and children, and between otherwise unconnected humans united by their humanity.
The examiner is not there to decide what is the "right" comparison for you to have drawn. There will certainly be other poems which might receive more comparisons, but the examiner's job is to look at what you have written and mark it based on what you have actually said and how well you have expressed yourself.