I am trying to explain to myself why Peter was not caught in the same bed as Ron, and I now wonder whether there is anyway to trick the map.
Is it possible to hide from the Marauders Map?
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From the Pottermore fact file on the Marauders' Map:
Shows the location of any person or ghost on Hogwart’s grounds, isn’t fooled by an Animagus or an Invisibility Cloak
As far as I can remember, there's no case in canon of anyone ever managing to hide from the map. It detected Peter Pettigrew when he was in rat form; it detected Barty Crouch Jr. when he was using Polyjuice Potion; it detected Harry Potter when he was under the Invisibility Cloak. If there's any concealing magic sufficiently powerful to bamboozle it, we never saw it in the books.
As for why Peter Pettigrew was never seen in the same bed as Ron, the simple solution is that among so many people in the castle, nobody noticed. The best way to avoid being detected using the Marauders' Map is simply to hope that the user of the map doesn't notice you. See also Why couldn't Harry or anybody else see Peter Pettigrew aka Scabbers on the Marauder's Map when Lupin could?, where the top answer has a quote from JKR as follows:
Why didn't Fred and George notice Peter Pettigrew on the Marauder's Map before ("Prisoner of Azkaban")?
It would not have mattered if they had. Unless somebody was very familiar with the story of Sirius Black (and after all, Sirius was not Mr. and Mrs. Weasley's best friend – indeed, they never knew him until after he escaped from Azkaban), Fred and George would be unlikely to know or remember that Peter Pettigrew was the person Sirius had (supposedly) murdered. Even if Fred and George HAD heard the story at some point, why would they assume that the 'Peter Pettigrew' they occasionally saw moving around the map was, in fact, the man murdered years before?
Fred and George used the map for their own mischief-making, so they concentrated, naturally enough, on those portions of the map where they were planning their next misdeeds. And finally, you must not forget that hundreds of little dots are moving around this map at any given time… Fred and George did not know everyone in school by name, so a single unfamiliar name was unlikely to stand out.
Although we never see any concealing magic which can fool the map, it's possible not to appear on it simply by being in a location which it doesn't cover. For instance, leaving Hogwarts (a trivial solution, since the map is a map of Hogwarts alone), or going to the Room of Requirement (apparently the magic which makes the Room undiscoverable is stronger than the magic which makes the map plot everything). As discussed in the top answer to Why didn't the Marauder's Map show Mad Eye Moody hidden in the trunk?, it's definitely true that the Room of Requirement doesn't show up on the map:
Although he consulted the map as often as he could, sometimes making unnecessary visits to the bathroom between lessons to search it, he did not once see Malfoy anywhere suspicious...at these times Malfoy was not only nowhere near them, but impossible to locate on the map at all. [...] And still there were those inexplicable times when Malfoy simply vanished from the map [...]
“I think it’ll be part of the magic of the room,” said Hermione. “If you need it to be Unplottable, it will be.”
-- HP and the Half-Blood Prince
It's kinda like air traffic control there are hundreds of dots on the map at any given time "flying" around the school so if Fred and George are the ATC they aren't going to notice an unusual plane unless it's transmitter is turned off in the schools case if Peter did something unusual to stand out which is likely why he never used his magic despite having the trace removed from his wand by Voldermort.
Then it (he) will stand out as the only one in the area with no flight info being displayed or fed THEN Fred and George would DEFINITELY without a doubt notice and do something about it.
In this case all the names just blended in together.
The map only show the teachers and anyone you look for specifically, which is why the map is not just black with all the names(of students), so if Harry was not looking on purpose, or if his thoughts were not on Peter, like Lupin's may have been(or drifted to), then it would not show. perhaps it also showed you anyone who you might subconsciously find suspicious, like Barty Crouch but perhaps this was because Harry was still unconsciously mad from Snape's accusation(about potion-ingredient theft). Also, things like the Pensieve and Moody's Trunk as well as the Room Of Requiement and the Chamber Of Secrets will not show up because of their particular magic.