Yes, there are known mass anomalies on Ganymede.
From Scientists Discover Ganymede has a Lumpy Interior Aug. 13, 2004
Scientists have discovered irregular lumps beneath the icy surface of Jupiter's largest moon, Ganymede. These irregular masses may be rock formations, supported by Ganymede's icy shell for billions of years. This discovery comes nearly a year after the orchestrated demise of NASA's Galileo spacecraft into Jupiter's atmosphere and more than seven years after the data were collected.
Unfortunately, the paper is paywalled, but here's the abstract.
Discovery of Mass Anomalies on Ganymede
JOHN D. ANDERSON , GERALD SCHUBERT, AND JENNIFER L. PALGUTA https://doi.org/10.1126/science.1099050
We present the discovery of mass anomalies on Ganymede, Jupiter's third and largest Galilean satellite. This discovery is surprising for such a large icy satellite. We used the radio Doppler data generated with the Galileo spacecraft during its second encounter with Ganymede on 6 September 1996 to model the mass anomalies. Two surface mass anomalies, one a positive mass at high latitude and the other a negative mass at low latitude, can explain the data. There are no obvious geological features that can be identified with the anomalies.
These mascons should not be a problem for JUICE, which is carrying plenty of fuel for the manoeuvres required to visit its targets.
Here's some more recent information on Ganymede's gravitational field, from Geophysical Research Letters, found by planetmaker.
Gravity Field of Ganymede After the Juno Extended Mission, 12 December 2022, by L. Gomez Casajus, A. I. Ermakov, M. Zannoni, J. T. Keane, D. Stevenson, D. R. Buccino, D. Durante, M. Parisi, R. S. Park, P. Tortora, S. J. Bolton
On 7 June 2021, Juno performed the first close flyby of Ganymede, the largest satellite of Jupiter (and the largest moon in the Solar System), since the end of the Galileo mission. The gravity field of Ganymede was reconstructed using the radio tracking data from all of the Ganymede encounters of both the Galileo and Juno missions. The data analysis hints at localized gravity anomalies. Interpretation of the gravity data suggests a slightly higher moment of inertia with respect previous publications, indicating a lesser degree of differentiation.
The gravity field of Ganymede derived from joint analysis of Galileo and Juno flyby data, computed on the reference sphere with radius 2,631.2 km. (a) The full gravity field solution, expanded to degree/order 5. Spacecraft ground tracks are shown in green (Galileo) and yellow (Juno). (b) gravity field solution, expanded to degree/order 5, removing completely the J2 and C22 terms. In b, the opacity of the gravity map is scaled by the signal-to-noise ratio. The white contours enclose regions with signal-to-noise ratio greater than 1 (dashed line contour) and 3 (solid line contour). All maps are in Mollweide projection, centered on the sub-Jupiter point. Latitude and longitude grid lines are in 30° intervals. Maps are draped over a color image mosaic of Ganymede (Collins et al., 2013).
The acceleration unit used in these figures is the Gal, which is equal to $1\,\mathrm{cm/s^2}$.
As well as the having the benefit of additional data of higher precision, this study used more powerful and sophisticated data analysis techniques than the study from 2004.
