Typically, GI symptoms are more prominent in children with influenza than adults but during the H1N1 epidemic in 2009 (which has subsequently become endemic), up to 26% of hospitalized adults with H1N1 infection had abdominal pain or vomiting and up to 25% had diarrhea (1). 

In fact, H1N1 virus has been isolated from stool of adult hospitalized patients (2,3) and receptors of influenza virus have been identified in human GI epithelial cells, the correlation between GI symptoms and isolation of virus from stool is poorly defined (4).

Interestingly, the mechanism involved in influenza-mediated intestinal injury may have less to do with direct invasion of the intestinal mucosa by the virus and more to do with immune mediated changes  related to alterations in the intestinal microbiota induced by influenza virus infection itself (4,5)! 

Aside from direct or indirect effects of influenza virus on the GI tract, oseltamivir and non-steroidal anti-inflammatory use may also contribute to GI symptoms (4).

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References

1. Writing Committee of the WHO Consultation on Clinical Aspects of Pandemic (H1N1) 2009 influenza. Clinical aspects of pandemic 2009 influenza A (H1N1) virus infection. N Engl J Med 2010;362:1708-19. https://www.ncbi.nlm.nih.gov/pubmed/20445182
2. Yoo SJ, Moon SJ, Kuak E-Y, et al. Frequent detection of pandemic (H1N1) 2009 virus in stools of hospitalized patients. J Clin Microbiol 2010; 48:2314-2315. https://www.ncbi.nlm.nih.gov/pubmed/20375236
3. Minodier L, Charrel RN, Ceccaldi PE, et al. Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know? Virol J 2015;12:215. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676820/
4. Shu Y, Li CK, Gao R, et al. Avian influenza A(H5N1) viruses can directly infect and replicate in human gut tissues. J Infect Dis 2010;201:1173-7. https://www.ncbi.nlm.nih.gov/pubmed/20210629
5. Wang J, Li F, Wei H, et al. Respiratory influenza virus infection induces intestinal immune injury via microbiota mediated Th17 cell-dependent inflammation. J Exp Med 2014;211:2397-2410. http://europepmc.org/article/PMC/4235643