user-1: Are monks allowed to be in the same room as a nun alone (not a laywoman)? 
Are monks allowed to be in the same room as a nun (considering the rule applies) while others a present?
Is there a specific rule in the Vinaya for this, if so please cite.
What should one do if one sees a monk alone with a female nun and it is not allowed (if that's a rule)? 

user111: Women should be aware that it is an offence against his discipline if a monk touches a woman. If offering something to a monk either place it in his bowl or on his special receiving cloth — never directly into his hands. Male visitors should be aware that women with shaved heads may prefer not to hand anything to or receive anything directly from you. Put it down first and let the other person pick it up.
Women must be careful entering rooms (such as the library) where a monk might be present; it is an offence for a monk to be alone with a woman in "a secluded place" -- more details here.
Nuns also come under women. So the same rule applies.
What should one do if one sees a monk alone with a female nun and it is not allowed
If it is indeed a closed room and if you think they will be receptive to your suggestions, ask the monk in a non-offensive way. ex:  "Bhante, I've heard about this Vinaya rule regarding closed rooms. Would you like me to keep the door open?".
Regardless of whether they agree or not, most important thing for you is to not to get upset. If you get upset, you fail no matter what other people do.

-1: <p>Are monks allowed to be in the same room as a nun alone (not a laywoman)? </p>

<p>Are monks allowed to be in the same room as a nun (considering the rule applies) while others a present?</p>

<p>Is there a specific rule in the Vinaya for this, if so please cite.</p>

<p>What should one do if one sees a monk alone with a female nun and it is not allowed (if that's a rule)? </p>
 111: <p>Women should be aware that it is an offence against his discipline if a monk touches a woman. If offering something to a monk either place it in his bowl or on his special receiving cloth — never directly into his hands. Male visitors should be aware that women with shaved heads may prefer not to hand anything to or receive anything directly from you. Put it down first and let the other person pick it up.</p>
<p>Women must be careful entering rooms (such as the library) where a monk might be present; it is an offence for a monk to be alone with a woman in &quot;a secluded place&quot; -- <a href="https://www.accesstoinsight.org/lib/authors/ariyesako/layguide.html#alone" rel="nofollow noreferrer">more details here</a>.</p>
<p>Nuns also come under women. So the same rule applies.</p>
<p><strong>What should one do if one sees a monk alone with a female nun and it is not allowed</strong></p>
<p>If it is indeed a closed room and if you think they will be receptive to your suggestions, ask the monk in a non-offensive way. ex:  &quot;Bhante, I've heard about this Vinaya rule regarding closed rooms. Would you like me to keep the door open?&quot;.</p>
<p>Regardless of whether they agree or not, most important thing for you is to not to get upset. If you get upset, you fail no matter what other people do.</p>
