Hello from JustAnswer.
Some of this does not make sense, but it is more complex than simply whether inflammation is present in the GI tract.
Most of the inflammation - esophagitis, gastritis, duodenitis - are typically due to acid irritation and/or a bacterial infection of the upper GI tract. There are some primary inflammatory conditions that can affect the upper GI tract. Although Crohn's disease primarily affects the ileum and colon, it is possible for Crohn's disease to cause inflammation anywhere in the GI tract (while ulcerative colitis will be limited to the colon). Diagnosing whether inflammation in the upper GI tract is due to Crohn's disease is usually by the pathologic examination of the biopsies, looking for a specific type of inflammation (the medical term would be noncaseating granulomatous inflammation). If the pathology examination did not identify such inflammation, then the inflammation in the upper GI tract is probably not from Crohn's disease.
The ileitis is a common component of Crohn's disease, and would be very suspicious in someone with the symptoms that you describe, particularly the blood in the stool. IBS does not directly cause blood in the stool. It is possible that the chronic diarrhea or constipation associated with IBS can lead to anal problems that can bleed, such as hemorrhoids or anal fissures. But if there is no evidence of an anal problem, there would be more of a concern that there is a more significant GI problem.
The pathology report will also usually see characteristic changes to suggest Crohn's dsease when it is the cause. But it is possible that it was not an optimal biopsy since the doctor could not get a good look at the ileum.
If you were my patient, I would typically refer you to a Gastroenterologist at this point.
There is another option - to ask for a second opinion on the pathologist examination of the biopsies.
If I can provide any additional information, please let me know.