This is the kind of question where I have to give a little spiel about how we can't find out all the facts of history. There is so much that we can't know, because for most of history we have only limited primary sources to go on, often made with other aims in mind than creating an impartial record of events. We will never know anything at all about the vast majority of people in medieval England beyond perhaps their names in a court record. When it comes to more prominent people, we know more details, but there's still so much we don't know. For instance, we often know about illegitimate children that kings had with mistresses who were noblewomen, but if they had liaisons with servant women and children resulted, there was likely to acknowledgement from the king and so nobody today can be aware of it.
The relationship between Isabella of France and Roger Mortimer falls into this gulf of "we can never know". The evidence for a romance basically comes down to the fact that he worked with her to depose her husband, and the fact that people said she was having an affair. I wrote an answer in an AMA at /r/fantasy that addresses why this is in issue, let me quote from it:
One area where we know this has happened is in the historical memory of various queens, generally when something has "gone wrong" during their rule and the blame has been placed upon them. All historical rulers' reputations have been used for various purposes - think about King Alfred's value as a symbol of Englishness in the nineteenth century, or Richard III as the villainous usurper in Shakespeare - but it tends to be particularly and regularly negative when it comes to queens. Maybe because when it's not negative, they tend to be forgotten unless they're extremely notable (e.g. Elizabeth I).
[...] And it's not limited to France - English queen consorts (with foreign backgrounds) faced similar treatment when they stepped outside the bounds of acceptable behavior. The two "she-wolves of France", Isabella (1295-1358) and Margaret (1430-1482) are excellent examples. Isabella spent most of her time as queen effecting diplomacy between opposing factions in the English court and then between England and France, but all of this is generally neglected in favor of her actions in opposing her husband, Edward II, by leading a revolt against him to bring their son to the throne following some pretty bad behavior on Edward's part - particularly because she was depicted as having an extramarital affair with Roger Mortimer at the time.
The romance between Isabella and Roger serves a purpose of making Isabella not just a bad queen for her rebellion despite years of being a very good queen by traditional standards, but a bad woman who dishonored her husband and engaged in sex without being married to her lover. The chronicler who recorded the rumor that she had been pregnant with Roger's child, Jean Froissart, worked under Edward III, Isabella's son, who deposed her in turn - there is a clear reason for him to lend credence to rumors that make Isabella an illegitimate, immoral queen. (And to do the same to Roger Mortimer, who had been executed. In fact, such a rumor could make it easier for Isabella to regain her reputation, as she eventually did, since it could be seen as Mortimer seducing her into unqueenly behavior.)
If Isabella and Roger did have a child, there is no evidence of it. She could perhaps have been pregnant and miscarried, but it would be incredibly difficult for a queen to hide a pregnancy and/or miscarriage from the large numbers of people who were constantly with her, from pages serving in the palace to ladies-in-waiting.