Trump's popularity during the 2016 campaign was closely correlated with Internet Research Agency bot activity. Every 25,000 retweets by IRA accounts predicted a 1% increase in opinion polls for Trump.

It's not so much that the research is "misleading" as people are misinterpreting the results of the study. The researchers were never trying to establish causality between IRA account activity and Trump's polling numbers, they were just examining the relationship. From the discussion section of the paper:

The result, a one percent poll increase for the Republican candidate for every 25,000 weekly re-tweets of IRA messages, raises two questions about the effect: one regarding the magnitude and one regarding its asymmetry.

Here we have tested prediction, not causality. It seems unlikely that 25,000 re-tweets could influence one percent of the electorate in isolation (Guess, et al., 2019; Allcott, et al., 2019), although this might be more plausible than presumed at first glance, given that only about four percent of viewed tweets result in re-retweets (Lee, et al., 2015), such that 25,000 re-tweets could imply about 500,000 exposures to those messages per week. It is more likely, however, that Twitter is just a subset of a larger disinformation campaign carried out on multiple social media platforms (Issac and Wakabayashi, 2017; Howard, et al., 2018), as well as spread through social contagion (Centola, 2010) and to other parts of the interconnected ‘media ecosystem’ including print, radio and television (Benkler, et al., 2018). In this way IRA disinformation can frame the debate, meaning many more people than those directly exposed can be affected (Jamieson, 2018).

Any correlation established by an observational study could be spurious. Though our main finding has proved robust and our time series analysis excludes reverse causation, there could still be a third variable driving the relationship between IRA Twitter success and U.S. election opinion polls. We controlled for one of these — the success of Donald Trump’s personal Twitter account — but there are others that are more difficult to measure; including exposure to the U.S domestic media.

The asymmetrical effect we observed could be because specific groups and media outlets were targeted by the IRA (Jamieson, 2018; Miller, 2019) and those media outlets were particularly susceptible to disinformation (Benkler, et al., 2018), leading to considerably more re-tweets from those targeted groups (Badawy, et al., 2018).

We use macro-level data to establish a link between exposure to IRA disinformation and changes in U.S. public opinion. However, using aggregated data means we cannot know the extent to which the participants in election polls were exposed to IRA disinformation. This may not matter once social contagion (Centola, 2010) and media ecosystem effects (Benkler, et al., 2018) are taken into consideration. Nonetheless, establishing individual-level causal mechanisms should be a priority (Gerber and Zavisca, 2016; Spaiser, et al., 2017).